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BT 15.000 718.042 Td /F2 21.0 Tf  [(Multiple sequence alignment: a major challenge to large-scale )] TJ ET
BT 15.000 693.094 Td /F2 21.0 Tf  [(phylogenetics)] TJ ET
Q
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BT 15.000 675.088 Td /F3 9.8 Tf  [(November 18, 2010)] TJ ET
BT 96.510 675.088 Td /F3 9.8 Tf  [(�)] TJ ET
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BT 101.385 675.088 Td /F3 9.8 Tf  [(Tree of Life)] TJ ET
BT 26.250 663.247 Td /F1 9.8 Tf  [(Kevin Liu)] TJ ET
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BT 66.352 663.247 Td /F1 9.8 Tf  [(, )] TJ ET
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BT 26.250 651.342 Td /F1 9.8 Tf  [(Liu K, Linder CR, Warnow T. Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLOS Currents )] TJ ET
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BT 26.250 610.335 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 590.381 Td /F1 9.8 Tf  [(Over the last decade, dramatic advances have been made in developing methods for large-scale phylogeny estimation, so that )] TJ ET
BT 26.250 578.476 Td /F1 9.8 Tf  [(it is now feasible for investigators with moderate computational resources to obtain reasonable solutions to maximum likelihood )] TJ ET
BT 26.250 566.571 Td /F1 9.8 Tf  [(and maximum parsimony, even for datasets with a few thousand sequences. There has also been progress on developing )] TJ ET
BT 26.250 554.667 Td /F1 9.8 Tf  [(methods for multiple sequence alignment, so that greater alignment accuracy \(and subsequent improvement in phylogenetic )] TJ ET
BT 26.250 542.762 Td /F1 9.8 Tf  [(accuracy\) is now possible through automated methods. However, these methods have not been tested under conditions that )] TJ ET
BT 26.250 530.857 Td /F1 9.8 Tf  [(reflect properties of datasets confronted by large-scale phylogenetic estimation projects. In this paper we report on a study that )] TJ ET
BT 26.250 518.952 Td /F1 9.8 Tf  [(compares several alignment methods on a benchmark collection of nucleotide sequence datasets of up to 78,132 sequences. )] TJ ET
BT 26.250 507.048 Td /F1 9.8 Tf  [(We show that as the number of sequences increases, the number of alignment methods that can analyze the datasets )] TJ ET
BT 26.250 495.143 Td /F1 9.8 Tf  [(decreases. Furthermore, the most accurate alignment methods are unable to analyze the very largest datasets we studied, so )] TJ ET
BT 26.250 483.238 Td /F1 9.8 Tf  [(that only moderately accurate alignment methods can be used on the largest datasets. As a result, alignments computed for )] TJ ET
BT 26.250 471.333 Td /F1 9.8 Tf  [(large datasets have relatively large error rates, and maximum likelihood phylogenies computed on these alignments also have )] TJ ET
BT 26.250 459.429 Td /F1 9.8 Tf  [(high error rates. Therefore, the estimation of highly accurate multiple sequence alignments is a major challenge for Tree of Life )] TJ ET
BT 26.250 447.524 Td /F1 9.8 Tf  [(projects, and more generally for large-scale systematics studies.)] TJ ET
BT 26.250 410.921 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 390.967 Td /F1 9.8 Tf  [(The research was supported by the US National Science Foundation DEB 0733029, and by Microsoft Research through )] TJ ET
BT 545.954 390.967 Td /F1 9.8 Tf  [(support )] TJ ET
BT 26.250 379.062 Td /F1 9.8 Tf  [(to TW.)] TJ ET
BT 26.250 349.960 Td /F4 12.0 Tf  [(Introduction)] TJ ET
BT 26.250 330.006 Td /F1 9.8 Tf  [(Species trees are typically estimated from a collection of genes \(or other genomic regions\), in one of two ways. The first way )] TJ ET
BT 26.250 318.101 Td /F1 9.8 Tf  [(produces alignments on each gene, and then runs a phylogeny estimation method on the concatenation of these alignments; )] TJ ET
BT 26.250 306.196 Td /F1 9.8 Tf  [(the second way estimates trees for each gene based upon an alignment of the sequences, and then combines these estimated )] TJ ET
BT 26.250 294.291 Td /F1 9.8 Tf  [(gene trees into a species tree. In both cases, therefore, the accuracy of the resultant species tree depends directly or indirectly )] TJ ET
BT 26.250 282.387 Td /F1 9.8 Tf  [(upon the alignments that are produced for each gene )] TJ ET
0.267 0.267 0.267 rg
BT 258.222 282.387 Td /F1 9.8 Tf  [([1] [2] [3] [4] [5] [6] [7])] TJ ET
0.271 0.267 0.267 rg
BT 350.379 282.387 Td /F1 9.8 Tf  [(. Because of the centrality of sequence alignment to )] TJ ET
BT 26.250 270.482 Td /F1 9.8 Tf  [(phylogenetics \(and other problems in biology\), many alignment methods have been developed. ClustalW )] TJ ET
0.267 0.267 0.267 rg
BT 480.366 270.482 Td /F1 9.8 Tf  [([8])] TJ ET
0.271 0.267 0.267 rg
BT 491.208 270.482 Td /F1 9.8 Tf  [( is perhaps the )] TJ ET
BT 26.250 258.577 Td /F1 9.8 Tf  [(most well known, and probably the most frequently used alignment method in systematics, but there are many others, including )] TJ ET
BT 26.250 246.672 Td /F1 9.8 Tf  [(MAFFT )] TJ ET
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BT 61.457 246.672 Td /F1 9.8 Tf  [([9])] TJ ET
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BT 72.299 246.672 Td /F1 9.8 Tf  [(, T-Coffee )] TJ ET
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BT 134.621 246.672 Td /F1 9.8 Tf  [(, Probcons )] TJ ET
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BT 183.937 246.672 Td /F1 9.8 Tf  [([11])] TJ ET
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BT 200.200 246.672 Td /F1 9.8 Tf  [(, POY )] TJ ET
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BT 245.186 246.672 Td /F1 9.8 Tf  [(, and Muscle )] TJ ET
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BT 303.170 246.672 Td /F1 9.8 Tf  [([13])] TJ ET
0.271 0.267 0.267 rg
BT 319.433 246.672 Td /F1 9.8 Tf  [(, that are used in the systematics community. There are )] TJ ET
BT 26.250 234.768 Td /F1 9.8 Tf  [(also newer methods, i.e., Opal )] TJ ET
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BT 160.644 234.768 Td /F1 9.8 Tf  [([14])] TJ ET
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BT 210.506 234.768 Td /F1 9.8 Tf  [([15])] TJ ET
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BT 226.769 234.768 Td /F1 9.8 Tf  [(, Prank+GT )] TJ ET
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BT 279.604 234.768 Td /F1 9.8 Tf  [([16])] TJ ET
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BT 295.867 234.768 Td /F1 9.8 Tf  [(, FSA )] TJ ET
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BT 322.962 234.768 Td /F1 9.8 Tf  [([17])] TJ ET
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BT 339.225 234.768 Td /F1 9.8 Tf  [(, POY* )] TJ ET
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BT 371.741 234.768 Td /F1 9.8 Tf  [([18])] TJ ET
0.271 0.267 0.267 rg
BT 388.004 234.768 Td /F1 9.8 Tf  [(, SATCHMO )] TJ ET
0.267 0.267 0.267 rg
BT 444.886 234.768 Td /F1 9.8 Tf  [([19])] TJ ET
0.271 0.267 0.267 rg
BT 461.149 234.768 Td /F1 9.8 Tf  [(, ProbAlign )] TJ ET
0.267 0.267 0.267 rg
BT 511.547 234.768 Td /F1 9.8 Tf  [([20])] TJ ET
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BT 527.810 234.768 Td /F1 9.8 Tf  [(, ProbTree )] TJ ET
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BT 26.250 222.863 Td /F1 9.8 Tf  [([21])] TJ ET
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BT 42.513 222.863 Td /F1 9.8 Tf  [(, BALi-Phy )] TJ ET
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BT 91.282 222.863 Td /F1 9.8 Tf  [([22])] TJ ET
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BT 107.546 222.863 Td /F1 9.8 Tf  [(, and SAT� )] TJ ET
0.267 0.267 0.267 rg
BT 159.035 222.863 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 175.298 222.863 Td /F1 9.8 Tf  [(, which have also been developed but are less frequently used.)] TJ ET
BT 26.250 203.458 Td /F1 9.8 Tf  [(Evaluations of these methods on both simulated and biological datasets show that alignment accuracy impacts tree accuracy, )] TJ ET
BT 26.250 191.553 Td /F1 9.8 Tf  [(and that some methods \(notably MAFFT and SAT�\) can produce highly accurate alignments on large datasets, and hence )] TJ ET
BT 26.250 179.649 Td /F1 9.8 Tf  [(make it possible to construct highly accurate trees when trees are computed using maximum likelihood \(ML\) )] TJ ET
0.267 0.267 0.267 rg
BT 494.416 179.649 Td /F1 9.8 Tf  [([7] [16])] TJ ET
0.271 0.267 0.267 rg
BT 524.231 179.649 Td /F1 9.8 Tf  [(. However, )] TJ ET
BT 26.250 167.744 Td /F1 9.8 Tf  [(these evaluations have been largely limited to datasets containing at most 1000 sequences, and so are not necessarily relevant )] TJ ET
BT 26.250 155.839 Td /F1 9.8 Tf  [(to large-scale systematics studies.)] TJ ET
BT 26.250 136.434 Td /F1 9.8 Tf  [(In this paper, we explore the performance of alignment methods on a collection of nucleotide datasets containing large numbers )] TJ ET
BT 26.250 124.530 Td /F1 9.8 Tf  [(of sequences. We report computational requirements, including running time and memory usage, and also the accuracy of the )] TJ ET
BT 26.250 112.625 Td /F1 9.8 Tf  [(alignments and of maximum likelihood \(ML\) trees estimated on these alignments.)] TJ ET
BT 26.250 93.220 Td /F1 9.8 Tf  [(These comparisons show striking differences between methods. Alignment methods differ in their computational requirements, )] TJ ET
BT 26.250 81.315 Td /F1 9.8 Tf  [(with some methods incapable of analyzing datasets beyond a few hundred sequences, and others able to analyze datasets with )] TJ ET
BT 26.250 69.411 Td /F1 9.8 Tf  [(tens of thousands of sequences. Running time and memory usage for some alignment methods can be enormous, sometimes )] TJ ET
BT 26.250 57.506 Td /F1 9.8 Tf  [(exceeding the computational requirements of RAxML )] TJ ET
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BT 258.183 57.506 Td /F1 9.8 Tf  [([23] [24])] TJ ET
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BT 293.419 57.506 Td /F1 9.8 Tf  [(, currently one of the most frequently used methods for large-)] TJ ET
BT 26.250 45.601 Td /F1 9.8 Tf  [(scale phylogenetic ML estimation. Methods also differ substantially with respect to alignment and subsequent tree accuracy, so )] TJ ET
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BT 15.000 718.042 Td /F2 21.0 Tf  [(Multiple sequence alignment: a major challenge to large-scale )] TJ ET
BT 15.000 693.094 Td /F2 21.0 Tf  [(phylogenetics)] TJ ET
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BT 15.000 675.088 Td /F3 9.8 Tf  [(November 18, 2010)] TJ ET
BT 96.510 675.088 Td /F3 9.8 Tf  [(�)] TJ ET
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BT 101.385 675.088 Td /F3 9.8 Tf  [(Tree of Life)] TJ ET
BT 26.250 663.247 Td /F1 9.8 Tf  [(Kevin Liu)] TJ ET
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BT 66.352 663.247 Td /F1 9.8 Tf  [(, )] TJ ET
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BT 71.773 663.247 Td /F1 9.8 Tf  [(C. Randal Linder)] TJ ET
0.271 0.267 0.267 rg
BT 144.927 663.247 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 150.348 663.247 Td /F1 9.8 Tf  [(Tandy Warnow)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 651.342 Td /F1 9.8 Tf  [(Liu K, Linder CR, Warnow T. Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLOS Currents )] TJ ET
BT 556.747 651.342 Td /F1 9.8 Tf  [(Tree )] TJ ET
BT 26.250 639.438 Td /F1 9.8 Tf  [(of Life. 2010 Nov 18 . Edition 1. doi: 10.1371/currents.RRN1198.)] TJ ET
q
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BT 26.250 610.335 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 590.381 Td /F1 9.8 Tf  [(Over the last decade, dramatic advances have been made in developing methods for large-scale phylogeny estimation, so that )] TJ ET
BT 26.250 578.476 Td /F1 9.8 Tf  [(it is now feasible for investigators with moderate computational resources to obtain reasonable solutions to maximum likelihood )] TJ ET
BT 26.250 566.571 Td /F1 9.8 Tf  [(and maximum parsimony, even for datasets with a few thousand sequences. There has also been progress on developing )] TJ ET
BT 26.250 554.667 Td /F1 9.8 Tf  [(methods for multiple sequence alignment, so that greater alignment accuracy \(and subsequent improvement in phylogenetic )] TJ ET
BT 26.250 542.762 Td /F1 9.8 Tf  [(accuracy\) is now possible through automated methods. However, these methods have not been tested under conditions that )] TJ ET
BT 26.250 530.857 Td /F1 9.8 Tf  [(reflect properties of datasets confronted by large-scale phylogenetic estimation projects. In this paper we report on a study that )] TJ ET
BT 26.250 518.952 Td /F1 9.8 Tf  [(compares several alignment methods on a benchmark collection of nucleotide sequence datasets of up to 78,132 sequences. )] TJ ET
BT 26.250 507.048 Td /F1 9.8 Tf  [(We show that as the number of sequences increases, the number of alignment methods that can analyze the datasets )] TJ ET
BT 26.250 495.143 Td /F1 9.8 Tf  [(decreases. Furthermore, the most accurate alignment methods are unable to analyze the very largest datasets we studied, so )] TJ ET
BT 26.250 483.238 Td /F1 9.8 Tf  [(that only moderately accurate alignment methods can be used on the largest datasets. As a result, alignments computed for )] TJ ET
BT 26.250 471.333 Td /F1 9.8 Tf  [(large datasets have relatively large error rates, and maximum likelihood phylogenies computed on these alignments also have )] TJ ET
BT 26.250 459.429 Td /F1 9.8 Tf  [(high error rates. Therefore, the estimation of highly accurate multiple sequence alignments is a major challenge for Tree of Life )] TJ ET
BT 26.250 447.524 Td /F1 9.8 Tf  [(projects, and more generally for large-scale systematics studies.)] TJ ET
BT 26.250 410.921 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 390.967 Td /F1 9.8 Tf  [(The research was supported by the US National Science Foundation DEB 0733029, and by Microsoft Research through )] TJ ET
BT 545.954 390.967 Td /F1 9.8 Tf  [(support )] TJ ET
BT 26.250 379.062 Td /F1 9.8 Tf  [(to TW.)] TJ ET
BT 26.250 349.960 Td /F4 12.0 Tf  [(Introduction)] TJ ET
BT 26.250 330.006 Td /F1 9.8 Tf  [(Species trees are typically estimated from a collection of genes \(or other genomic regions\), in one of two ways. The first way )] TJ ET
BT 26.250 318.101 Td /F1 9.8 Tf  [(produces alignments on each gene, and then runs a phylogeny estimation method on the concatenation of these alignments; )] TJ ET
BT 26.250 306.196 Td /F1 9.8 Tf  [(the second way estimates trees for each gene based upon an alignment of the sequences, and then combines these estimated )] TJ ET
BT 26.250 294.291 Td /F1 9.8 Tf  [(gene trees into a species tree. In both cases, therefore, the accuracy of the resultant species tree depends directly or indirectly )] TJ ET
BT 26.250 282.387 Td /F1 9.8 Tf  [(upon the alignments that are produced for each gene )] TJ ET
0.267 0.267 0.267 rg
BT 258.222 282.387 Td /F1 9.8 Tf  [([1] [2] [3] [4] [5] [6] [7])] TJ ET
0.271 0.267 0.267 rg
BT 350.379 282.387 Td /F1 9.8 Tf  [(. Because of the centrality of sequence alignment to )] TJ ET
BT 26.250 270.482 Td /F1 9.8 Tf  [(phylogenetics \(and other problems in biology\), many alignment methods have been developed. ClustalW )] TJ ET
0.267 0.267 0.267 rg
BT 480.366 270.482 Td /F1 9.8 Tf  [([8])] TJ ET
0.271 0.267 0.267 rg
BT 491.208 270.482 Td /F1 9.8 Tf  [( is perhaps the )] TJ ET
BT 26.250 258.577 Td /F1 9.8 Tf  [(most well known, and probably the most frequently used alignment method in systematics, but there are many others, including )] TJ ET
BT 26.250 246.672 Td /F1 9.8 Tf  [(MAFFT )] TJ ET
0.267 0.267 0.267 rg
BT 61.457 246.672 Td /F1 9.8 Tf  [([9])] TJ ET
0.271 0.267 0.267 rg
BT 72.299 246.672 Td /F1 9.8 Tf  [(, T-Coffee )] TJ ET
0.267 0.267 0.267 rg
BT 118.358 246.672 Td /F1 9.8 Tf  [([10])] TJ ET
0.271 0.267 0.267 rg
BT 134.621 246.672 Td /F1 9.8 Tf  [(, Probcons )] TJ ET
0.267 0.267 0.267 rg
BT 183.937 246.672 Td /F1 9.8 Tf  [([11])] TJ ET
0.271 0.267 0.267 rg
BT 200.200 246.672 Td /F1 9.8 Tf  [(, POY )] TJ ET
0.267 0.267 0.267 rg
BT 228.923 246.672 Td /F1 9.8 Tf  [([12])] TJ ET
0.271 0.267 0.267 rg
BT 245.186 246.672 Td /F1 9.8 Tf  [(, and Muscle )] TJ ET
0.267 0.267 0.267 rg
BT 303.170 246.672 Td /F1 9.8 Tf  [([13])] TJ ET
0.271 0.267 0.267 rg
BT 319.433 246.672 Td /F1 9.8 Tf  [(, that are used in the systematics community. There are )] TJ ET
BT 26.250 234.768 Td /F1 9.8 Tf  [(also newer methods, i.e., Opal )] TJ ET
0.267 0.267 0.267 rg
BT 160.644 234.768 Td /F1 9.8 Tf  [([14])] TJ ET
0.271 0.267 0.267 rg
BT 176.907 234.768 Td /F1 9.8 Tf  [(, Prank )] TJ ET
0.267 0.267 0.267 rg
BT 210.506 234.768 Td /F1 9.8 Tf  [([15])] TJ ET
0.271 0.267 0.267 rg
BT 226.769 234.768 Td /F1 9.8 Tf  [(, Prank+GT )] TJ ET
0.267 0.267 0.267 rg
BT 279.604 234.768 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 295.867 234.768 Td /F1 9.8 Tf  [(, FSA )] TJ ET
0.267 0.267 0.267 rg
BT 322.962 234.768 Td /F1 9.8 Tf  [([17])] TJ ET
0.271 0.267 0.267 rg
BT 339.225 234.768 Td /F1 9.8 Tf  [(, POY* )] TJ ET
0.267 0.267 0.267 rg
BT 371.741 234.768 Td /F1 9.8 Tf  [([18])] TJ ET
0.271 0.267 0.267 rg
BT 388.004 234.768 Td /F1 9.8 Tf  [(, SATCHMO )] TJ ET
0.267 0.267 0.267 rg
BT 444.886 234.768 Td /F1 9.8 Tf  [([19])] TJ ET
0.271 0.267 0.267 rg
BT 461.149 234.768 Td /F1 9.8 Tf  [(, ProbAlign )] TJ ET
0.267 0.267 0.267 rg
BT 511.547 234.768 Td /F1 9.8 Tf  [([20])] TJ ET
0.271 0.267 0.267 rg
BT 527.810 234.768 Td /F1 9.8 Tf  [(, ProbTree )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 222.863 Td /F1 9.8 Tf  [([21])] TJ ET
0.271 0.267 0.267 rg
BT 42.513 222.863 Td /F1 9.8 Tf  [(, BALi-Phy )] TJ ET
0.267 0.267 0.267 rg
BT 91.282 222.863 Td /F1 9.8 Tf  [([22])] TJ ET
0.271 0.267 0.267 rg
BT 107.546 222.863 Td /F1 9.8 Tf  [(, and SAT� )] TJ ET
0.267 0.267 0.267 rg
BT 159.035 222.863 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 175.298 222.863 Td /F1 9.8 Tf  [(, which have also been developed but are less frequently used.)] TJ ET
BT 26.250 203.458 Td /F1 9.8 Tf  [(Evaluations of these methods on both simulated and biological datasets show that alignment accuracy impacts tree accuracy, )] TJ ET
BT 26.250 191.553 Td /F1 9.8 Tf  [(and that some methods \(notably MAFFT and SAT�\) can produce highly accurate alignments on large datasets, and hence )] TJ ET
BT 26.250 179.649 Td /F1 9.8 Tf  [(make it possible to construct highly accurate trees when trees are computed using maximum likelihood \(ML\) )] TJ ET
0.267 0.267 0.267 rg
BT 494.416 179.649 Td /F1 9.8 Tf  [([7] [16])] TJ ET
0.271 0.267 0.267 rg
BT 524.231 179.649 Td /F1 9.8 Tf  [(. However, )] TJ ET
BT 26.250 167.744 Td /F1 9.8 Tf  [(these evaluations have been largely limited to datasets containing at most 1000 sequences, and so are not necessarily relevant )] TJ ET
BT 26.250 155.839 Td /F1 9.8 Tf  [(to large-scale systematics studies.)] TJ ET
BT 26.250 136.434 Td /F1 9.8 Tf  [(In this paper, we explore the performance of alignment methods on a collection of nucleotide datasets containing large numbers )] TJ ET
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BT 26.250 610.335 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 590.381 Td /F1 9.8 Tf  [(Over the last decade, dramatic advances have been made in developing methods for large-scale phylogeny estimation, so that )] TJ ET
BT 26.250 578.476 Td /F1 9.8 Tf  [(it is now feasible for investigators with moderate computational resources to obtain reasonable solutions to maximum likelihood )] TJ ET
BT 26.250 566.571 Td /F1 9.8 Tf  [(and maximum parsimony, even for datasets with a few thousand sequences. There has also been progress on developing )] TJ ET
BT 26.250 554.667 Td /F1 9.8 Tf  [(methods for multiple sequence alignment, so that greater alignment accuracy \(and subsequent improvement in phylogenetic )] TJ ET
BT 26.250 542.762 Td /F1 9.8 Tf  [(accuracy\) is now possible through automated methods. However, these methods have not been tested under conditions that )] TJ ET
BT 26.250 530.857 Td /F1 9.8 Tf  [(reflect properties of datasets confronted by large-scale phylogenetic estimation projects. In this paper we report on a study that )] TJ ET
BT 26.250 518.952 Td /F1 9.8 Tf  [(compares several alignment methods on a benchmark collection of nucleotide sequence datasets of up to 78,132 sequences. )] TJ ET
BT 26.250 507.048 Td /F1 9.8 Tf  [(We show that as the number of sequences increases, the number of alignment methods that can analyze the datasets )] TJ ET
BT 26.250 495.143 Td /F1 9.8 Tf  [(decreases. Furthermore, the most accurate alignment methods are unable to analyze the very largest datasets we studied, so )] TJ ET
BT 26.250 483.238 Td /F1 9.8 Tf  [(that only moderately accurate alignment methods can be used on the largest datasets. As a result, alignments computed for )] TJ ET
BT 26.250 471.333 Td /F1 9.8 Tf  [(large datasets have relatively large error rates, and maximum likelihood phylogenies computed on these alignments also have )] TJ ET
BT 26.250 459.429 Td /F1 9.8 Tf  [(high error rates. Therefore, the estimation of highly accurate multiple sequence alignments is a major challenge for Tree of Life )] TJ ET
BT 26.250 447.524 Td /F1 9.8 Tf  [(projects, and more generally for large-scale systematics studies.)] TJ ET
BT 26.250 410.921 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 390.967 Td /F1 9.8 Tf  [(The research was supported by the US National Science Foundation DEB 0733029, and by Microsoft Research through )] TJ ET
BT 545.954 390.967 Td /F1 9.8 Tf  [(support )] TJ ET
BT 26.250 379.062 Td /F1 9.8 Tf  [(to TW.)] TJ ET
BT 26.250 349.960 Td /F4 12.0 Tf  [(Introduction)] TJ ET
BT 26.250 330.006 Td /F1 9.8 Tf  [(Species trees are typically estimated from a collection of genes \(or other genomic regions\), in one of two ways. The first way )] TJ ET
BT 26.250 318.101 Td /F1 9.8 Tf  [(produces alignments on each gene, and then runs a phylogeny estimation method on the concatenation of these alignments; )] TJ ET
BT 26.250 306.196 Td /F1 9.8 Tf  [(the second way estimates trees for each gene based upon an alignment of the sequences, and then combines these estimated )] TJ ET
BT 26.250 294.291 Td /F1 9.8 Tf  [(gene trees into a species tree. In both cases, therefore, the accuracy of the resultant species tree depends directly or indirectly )] TJ ET
BT 26.250 282.387 Td /F1 9.8 Tf  [(upon the alignments that are produced for each gene )] TJ ET
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BT 258.222 282.387 Td /F1 9.8 Tf  [([1] [2] [3] [4] [5] [6] [7])] TJ ET
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BT 350.379 282.387 Td /F1 9.8 Tf  [(. Because of the centrality of sequence alignment to )] TJ ET
BT 26.250 270.482 Td /F1 9.8 Tf  [(phylogenetics \(and other problems in biology\), many alignment methods have been developed. ClustalW )] TJ ET
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BT 480.366 270.482 Td /F1 9.8 Tf  [([8])] TJ ET
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BT 491.208 270.482 Td /F1 9.8 Tf  [( is perhaps the )] TJ ET
BT 26.250 258.577 Td /F1 9.8 Tf  [(most well known, and probably the most frequently used alignment method in systematics, but there are many others, including )] TJ ET
BT 26.250 246.672 Td /F1 9.8 Tf  [(MAFFT )] TJ ET
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BT 134.621 246.672 Td /F1 9.8 Tf  [(, Probcons )] TJ ET
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BT 183.937 246.672 Td /F1 9.8 Tf  [([11])] TJ ET
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BT 245.186 246.672 Td /F1 9.8 Tf  [(, and Muscle )] TJ ET
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BT 303.170 246.672 Td /F1 9.8 Tf  [([13])] TJ ET
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BT 319.433 246.672 Td /F1 9.8 Tf  [(, that are used in the systematics community. There are )] TJ ET
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BT 175.298 222.863 Td /F1 9.8 Tf  [(, which have also been developed but are less frequently used.)] TJ ET
BT 26.250 203.458 Td /F1 9.8 Tf  [(Evaluations of these methods on both simulated and biological datasets show that alignment accuracy impacts tree accuracy, )] TJ ET
BT 26.250 191.553 Td /F1 9.8 Tf  [(and that some methods \(notably MAFFT and SAT�\) can produce highly accurate alignments on large datasets, and hence )] TJ ET
BT 26.250 179.649 Td /F1 9.8 Tf  [(make it possible to construct highly accurate trees when trees are computed using maximum likelihood \(ML\) )] TJ ET
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BT 494.416 179.649 Td /F1 9.8 Tf  [([7] [16])] TJ ET
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BT 524.231 179.649 Td /F1 9.8 Tf  [(. However, )] TJ ET
BT 26.250 167.744 Td /F1 9.8 Tf  [(these evaluations have been largely limited to datasets containing at most 1000 sequences, and so are not necessarily relevant )] TJ ET
BT 26.250 155.839 Td /F1 9.8 Tf  [(to large-scale systematics studies.)] TJ ET
BT 26.250 136.434 Td /F1 9.8 Tf  [(In this paper, we explore the performance of alignment methods on a collection of nucleotide datasets containing large numbers )] TJ ET
BT 26.250 124.530 Td /F1 9.8 Tf  [(of sequences. We report computational requirements, including running time and memory usage, and also the accuracy of the )] TJ ET
BT 26.250 112.625 Td /F1 9.8 Tf  [(alignments and of maximum likelihood \(ML\) trees estimated on these alignments.)] TJ ET
BT 26.250 93.220 Td /F1 9.8 Tf  [(These comparisons show striking differences between methods. Alignment methods differ in their computational requirements, )] TJ ET
BT 26.250 81.315 Td /F1 9.8 Tf  [(with some methods incapable of analyzing datasets beyond a few hundred sequences, and others able to analyze datasets with )] TJ ET
BT 26.250 69.411 Td /F1 9.8 Tf  [(tens of thousands of sequences. Running time and memory usage for some alignment methods can be enormous, sometimes )] TJ ET
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0.267 0.267 0.267 rg
BT 258.183 57.506 Td /F1 9.8 Tf  [([23] [24])] TJ ET
0.271 0.267 0.267 rg
BT 293.419 57.506 Td /F1 9.8 Tf  [(, currently one of the most frequently used methods for large-)] TJ ET
BT 26.250 45.601 Td /F1 9.8 Tf  [(scale phylogenetic ML estimation. Methods also differ substantially with respect to alignment and subsequent tree accuracy, so )] TJ ET
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BT 26.250 767.476 Td /F1 9.8 Tf  [(that the selection of alignment method is very important to the systematics study.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(The main observation in this study is that only a small number of multiple sequence alignment methods can be run on datasets )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(with several thousand sequences. Furthermore, of those methods that can be run on large datasets, none produces alignments )] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(of sufficient accuracy to be useful in estimating highly accurate phylogenies. Therefore, when datasets are large and have )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(evolved with many indels, the input to species tree estimations \(i.e. either super-alignments or gene trees\) are likely to be of )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(poor accuracy; consequently, this suggests that species tree estimates will also have reduced accuracy for large datasets, )] TJ ET
BT 26.250 688.548 Td /F1 9.8 Tf  [(directly because of alignment difficulties.)] TJ ET
BT 26.250 651.945 Td /F4 12.0 Tf  [(Methodology)] TJ ET
BT 26.250 631.991 Td /F4 9.8 Tf  [(Overview)] TJ ET
BT 26.250 612.586 Td /F1 9.8 Tf  [(We used several rRNA biological datasets \(of up to 27,643 sequences\) and one simulated dataset \(of 78,132 sequences\) to )] TJ ET
BT 26.250 600.681 Td /F1 9.8 Tf  [(evaluate the alignment methods. The biological datasets have curated alignments based upon secondary structure and )] TJ ET
BT 26.250 588.777 Td /F1 9.8 Tf  [(reference trees produced by computing maximum likelihood trees with bootstrapping on each curated alignment, retaining only )] TJ ET
BT 26.250 576.872 Td /F1 9.8 Tf  [(the high support edges. For the simulated dataset, we have the true alignment and true tree. See Table 1 and the )] TJ ET
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BT 180.144 564.967 Td /F1 9.8 Tf  [( for details about these data.)] TJ ET
BT 26.250 545.562 Td /F1 9.8 Tf  [(For each dataset, we attempted to compute alignments using a collection of alignment methods, and for each alignment that we )] TJ ET
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BT 26.250 509.848 Td /F1 9.8 Tf  [(the true or reference tree to determine the tree error rate. We also recorded running time for each analysis.)] TJ ET
BT 26.250 490.443 Td /F4 9.8 Tf  [(Datasets)] TJ ET
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0.271 0.267 0.267 rg
BT 435.321 471.039 Td /F1 9.8 Tf  [( and have curated alignments )] TJ ET
BT 26.250 459.134 Td /F1 9.8 Tf  [(based upon secondary structure. While secondary structure alignments are highly reliable, there is no guarantee that these are )] TJ ET
BT 26.250 447.229 Td /F1 9.8 Tf  [(perfectly correct. However, these are the most reliable benchmarks available to date for testing nucleotide alignment methods, )] TJ ET
BT 26.250 435.324 Td /F1 9.8 Tf  [(other than using simulated data. These biological datasets contain 16S and 23S sequences, markers that are frequently used )] TJ ET
BT 26.250 423.420 Td /F1 9.8 Tf  [(for estimating phylogenies. They range in size from about 100 sequences to almost 28,000 sequences. We used the )] TJ ET
BT 26.250 411.515 Td /F1 9.8 Tf  [(preprocessing steps in )] TJ ET
0.267 0.267 0.267 rg
BT 126.499 411.515 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 142.762 411.515 Td /F1 9.8 Tf  [( on these datasets to remove taxa that were more than 50% unsequenced, and to remove illegal )] TJ ET
BT 26.250 399.610 Td /F1 9.8 Tf  [(characters. The empirical statistics for the resulting curated alignments after preprocessing are listed in Table 1. Note that these )] TJ ET
BT 26.250 387.705 Td /F1 9.8 Tf  [(biological datasets are relatively �gappy�, with indels occupying 60-90% of the curated alignment matrix. They also have )] TJ ET
BT 26.250 375.801 Td /F1 9.8 Tf  [(different gap length distributions, and different average and maximum p-distances. Thus, these datasets have properties that )] TJ ET
BT 26.250 363.896 Td /F1 9.8 Tf  [(are challenging for alignment and phylogeny estimation, and are realistic examples of datasets used in large-scale phylogenetic )] TJ ET
BT 26.250 351.991 Td /F1 9.8 Tf  [(studies. See the Supplementary Materials online webpage )] TJ ET
0.267 0.267 0.267 rg
BT 280.413 351.991 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 296.676 351.991 Td /F1 9.8 Tf  [( for these data.)] TJ ET
BT 26.250 332.586 Td /F1 9.8 Tf  [(The simulated dataset was obtained from )] TJ ET
0.267 0.267 0.267 rg
BT 207.249 332.586 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 223.512 332.586 Td /F1 9.8 Tf  [(, with 78,132 DNA sequences and 1,287 sites in the true alignment. This dataset )] TJ ET
BT 26.250 320.682 Td /F1 9.8 Tf  [(is the last replicate from the simulation by )] TJ ET
0.267 0.267 0.267 rg
BT 207.775 320.682 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 224.038 320.682 Td /F1 9.8 Tf  [(, obtained at http://www.microbesonline.org/fasttree/; we call this the �Price 78K� )] TJ ET
BT 26.250 308.777 Td /F1 9.8 Tf  [(dataset. The empirical statistics for the true alignment on this dataset are in Table 1. Many of the empirical statistics for the )] TJ ET
BT 26.250 296.872 Td /F1 9.8 Tf  [(Price 78K dataset are similar to those of the empirical datasets; however, the Price 78K dataset has hardly any indels \(in fact )] TJ ET
BT 26.250 284.967 Td /F1 9.8 Tf  [(the gappiness is two orders of magnitude less than those exhibited in the biological datasets\) and the average gap length is )] TJ ET
BT 26.250 273.063 Td /F1 9.8 Tf  [(extremely short. As a result, the Price 78K dataset is potentially easier to align than the biological datasets. Because of its size, )] TJ ET
BT 26.250 261.158 Td /F1 9.8 Tf  [(however, the Price 78K dataset provides a test of scalability.)] TJ ET
BT 26.250 241.753 Td /F1 9.8 Tf  [(Reference alignments and trees were computed as follows. For the Price 78K dataset, we used the true alignment as the )] TJ ET
BT 26.250 229.848 Td /F1 9.8 Tf  [(reference alignment, and the true tree as the reference tree; these are known because the Price 78K dataset is simulated. For )] TJ ET
BT 26.250 217.944 Td /F1 9.8 Tf  [(the biological datasets, the curated alignment, modified by our minor cleaning operations, is the reference alignment. We )] TJ ET
BT 26.250 206.039 Td /F1 9.8 Tf  [(computed unaligned sequences from the reference alignments by simply deleting indels \(�-�\). To obtain reference trees for the )] TJ ET
BT 26.250 194.134 Td /F1 9.8 Tf  [(biological datasets, we performed rapid bootstrapping analyses with RAxML )] TJ ET
0.267 0.267 0.267 rg
BT 356.258 194.134 Td /F1 9.8 Tf  [([29])] TJ ET
0.271 0.267 0.267 rg
BT 372.521 194.134 Td /F1 9.8 Tf  [( on the curated alignment to produce a tree )] TJ ET
BT 26.250 182.229 Td /F1 9.8 Tf  [(with support values, and then contracted all edges with less than 75% support. We generated 500 bootstrap replicates on all )] TJ ET
BT 26.250 170.325 Td /F1 9.8 Tf  [(datasets except for the two largest biological datasets, 16S.T and 16S.B.ALL, for which we used 346 and 573 bootstrap )] TJ ET
BT 26.250 158.420 Td /F1 9.8 Tf  [(replicates, respectively.)] TJ ET
BT 26.250 139.015 Td /F4 9.8 Tf  [(Table 1: Empirical statistics for reference alignments and reference trees for each dataset.)] TJ ET
BT 444.028 139.015 Td /F1 9.8 Tf  [( �# Taxa� is the number of )] TJ ET
BT 26.250 127.110 Td /F1 9.8 Tf  [(taxa. �# Sites� is the number of sites in the reference alignment, which is the curated alignment for the CRW datasets and the )] TJ ET
BT 26.250 115.206 Td /F1 9.8 Tf  [(true alignment for the Price 78K dataset. �Indels� is the percentage of cells in the reference alignment matrix that consist of )] TJ ET
BT 26.250 103.301 Td /F1 9.8 Tf  [(indels. �Res� is the resolution of the reference tree, or the percentage of internal edges present in the reference tree out of the )] TJ ET
BT 26.250 91.396 Td /F1 9.8 Tf  [(total possible number of edges. The p-distance between two sequences is the percentage of sites in which the two sequences )] TJ ET
BT 26.250 79.491 Td /F1 9.8 Tf  [(have different nucleotides, and is denoted by �p-dist�. �Avg p-dist� is the average p-distance across all pairs of sequences in the )] TJ ET
BT 26.250 67.587 Td /F1 9.8 Tf  [(reference alignment, and �Max p-dist� is the maximum p-distance across all pairs of sequences in the reference alignment. �Gap )] TJ ET
BT 26.250 55.682 Td /F1 9.8 Tf  [(Len� is the average length of a gap \(contiguous string of indels\) in the reference alignment. n=1 for all reported values.)] TJ ET
1.000 1.000 1.000 rg
26.250 44.301 555.000 1.500 re f
Q
q
15.000 44.301 577.500 732.699 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(that the selection of alignment method is very important to the systematics study.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(The main observation in this study is that only a small number of multiple sequence alignment methods can be run on datasets )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(with several thousand sequences. Furthermore, of those methods that can be run on large datasets, none produces alignments )] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(of sufficient accuracy to be useful in estimating highly accurate phylogenies. Therefore, when datasets are large and have )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(evolved with many indels, the input to species tree estimations \(i.e. either super-alignments or gene trees\) are likely to be of )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(poor accuracy; consequently, this suggests that species tree estimates will also have reduced accuracy for large datasets, )] TJ ET
BT 26.250 688.548 Td /F1 9.8 Tf  [(directly because of alignment difficulties.)] TJ ET
BT 26.250 651.945 Td /F4 12.0 Tf  [(Methodology)] TJ ET
BT 26.250 631.991 Td /F4 9.8 Tf  [(Overview)] TJ ET
BT 26.250 612.586 Td /F1 9.8 Tf  [(We used several rRNA biological datasets \(of up to 27,643 sequences\) and one simulated dataset \(of 78,132 sequences\) to )] TJ ET
BT 26.250 600.681 Td /F1 9.8 Tf  [(evaluate the alignment methods. The biological datasets have curated alignments based upon secondary structure and )] TJ ET
BT 26.250 588.777 Td /F1 9.8 Tf  [(reference trees produced by computing maximum likelihood trees with bootstrapping on each curated alignment, retaining only )] TJ ET
BT 26.250 576.872 Td /F1 9.8 Tf  [(the high support edges. For the simulated dataset, we have the true alignment and true tree. See Table 1 and the )] TJ ET
BT 26.250 564.967 Td /F1 9.8 Tf  [(supplementary online materials )] TJ ET
0.267 0.267 0.267 rg
BT 163.881 564.967 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 180.144 564.967 Td /F1 9.8 Tf  [( for details about these data.)] TJ ET
BT 26.250 545.562 Td /F1 9.8 Tf  [(For each dataset, we attempted to compute alignments using a collection of alignment methods, and for each alignment that we )] TJ ET
BT 26.250 533.658 Td /F1 9.8 Tf  [(generated, we computed a maximum likelihood tree using either RAxML or FastTree )] TJ ET
0.267 0.267 0.267 rg
BT 393.094 533.658 Td /F1 9.8 Tf  [([26] [27])] TJ ET
0.271 0.267 0.267 rg
BT 428.330 533.658 Td /F1 9.8 Tf  [(. We compared the estimated )] TJ ET
BT 26.250 521.753 Td /F1 9.8 Tf  [(alignments to the true or curated alignment to determine the alignment error rate, and we compared the estimated ML tree to )] TJ ET
BT 26.250 509.848 Td /F1 9.8 Tf  [(the true or reference tree to determine the tree error rate. We also recorded running time for each analysis.)] TJ ET
BT 26.250 490.443 Td /F4 9.8 Tf  [(Datasets)] TJ ET
BT 26.250 471.039 Td /F1 9.8 Tf  [(The biological datasets were drawn from Robin Gutell�s Comparative RNA Website \(CRW\) )] TJ ET
0.267 0.267 0.267 rg
BT 419.058 471.039 Td /F1 9.8 Tf  [([28])] TJ ET
0.271 0.267 0.267 rg
BT 435.321 471.039 Td /F1 9.8 Tf  [( and have curated alignments )] TJ ET
BT 26.250 459.134 Td /F1 9.8 Tf  [(based upon secondary structure. While secondary structure alignments are highly reliable, there is no guarantee that these are )] TJ ET
BT 26.250 447.229 Td /F1 9.8 Tf  [(perfectly correct. However, these are the most reliable benchmarks available to date for testing nucleotide alignment methods, )] TJ ET
BT 26.250 435.324 Td /F1 9.8 Tf  [(other than using simulated data. These biological datasets contain 16S and 23S sequences, markers that are frequently used )] TJ ET
BT 26.250 423.420 Td /F1 9.8 Tf  [(for estimating phylogenies. They range in size from about 100 sequences to almost 28,000 sequences. We used the )] TJ ET
BT 26.250 411.515 Td /F1 9.8 Tf  [(preprocessing steps in )] TJ ET
0.267 0.267 0.267 rg
BT 126.499 411.515 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 142.762 411.515 Td /F1 9.8 Tf  [( on these datasets to remove taxa that were more than 50% unsequenced, and to remove illegal )] TJ ET
BT 26.250 399.610 Td /F1 9.8 Tf  [(characters. The empirical statistics for the resulting curated alignments after preprocessing are listed in Table 1. Note that these )] TJ ET
BT 26.250 387.705 Td /F1 9.8 Tf  [(biological datasets are relatively �gappy�, with indels occupying 60-90% of the curated alignment matrix. They also have )] TJ ET
BT 26.250 375.801 Td /F1 9.8 Tf  [(different gap length distributions, and different average and maximum p-distances. Thus, these datasets have properties that )] TJ ET
BT 26.250 363.896 Td /F1 9.8 Tf  [(are challenging for alignment and phylogeny estimation, and are realistic examples of datasets used in large-scale phylogenetic )] TJ ET
BT 26.250 351.991 Td /F1 9.8 Tf  [(studies. See the Supplementary Materials online webpage )] TJ ET
0.267 0.267 0.267 rg
BT 280.413 351.991 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 296.676 351.991 Td /F1 9.8 Tf  [( for these data.)] TJ ET
BT 26.250 332.586 Td /F1 9.8 Tf  [(The simulated dataset was obtained from )] TJ ET
0.267 0.267 0.267 rg
BT 207.249 332.586 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 223.512 332.586 Td /F1 9.8 Tf  [(, with 78,132 DNA sequences and 1,287 sites in the true alignment. This dataset )] TJ ET
BT 26.250 320.682 Td /F1 9.8 Tf  [(is the last replicate from the simulation by )] TJ ET
0.267 0.267 0.267 rg
BT 207.775 320.682 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 224.038 320.682 Td /F1 9.8 Tf  [(, obtained at http://www.microbesonline.org/fasttree/; we call this the �Price 78K� )] TJ ET
BT 26.250 308.777 Td /F1 9.8 Tf  [(dataset. The empirical statistics for the true alignment on this dataset are in Table 1. Many of the empirical statistics for the )] TJ ET
BT 26.250 296.872 Td /F1 9.8 Tf  [(Price 78K dataset are similar to those of the empirical datasets; however, the Price 78K dataset has hardly any indels \(in fact )] TJ ET
BT 26.250 284.967 Td /F1 9.8 Tf  [(the gappiness is two orders of magnitude less than those exhibited in the biological datasets\) and the average gap length is )] TJ ET
BT 26.250 273.063 Td /F1 9.8 Tf  [(extremely short. As a result, the Price 78K dataset is potentially easier to align than the biological datasets. Because of its size, )] TJ ET
BT 26.250 261.158 Td /F1 9.8 Tf  [(however, the Price 78K dataset provides a test of scalability.)] TJ ET
BT 26.250 241.753 Td /F1 9.8 Tf  [(Reference alignments and trees were computed as follows. For the Price 78K dataset, we used the true alignment as the )] TJ ET
BT 26.250 229.848 Td /F1 9.8 Tf  [(reference alignment, and the true tree as the reference tree; these are known because the Price 78K dataset is simulated. For )] TJ ET
BT 26.250 217.944 Td /F1 9.8 Tf  [(the biological datasets, the curated alignment, modified by our minor cleaning operations, is the reference alignment. We )] TJ ET
BT 26.250 206.039 Td /F1 9.8 Tf  [(computed unaligned sequences from the reference alignments by simply deleting indels \(�-�\). To obtain reference trees for the )] TJ ET
BT 26.250 194.134 Td /F1 9.8 Tf  [(biological datasets, we performed rapid bootstrapping analyses with RAxML )] TJ ET
0.267 0.267 0.267 rg
BT 356.258 194.134 Td /F1 9.8 Tf  [([29])] TJ ET
0.271 0.267 0.267 rg
BT 372.521 194.134 Td /F1 9.8 Tf  [( on the curated alignment to produce a tree )] TJ ET
BT 26.250 182.229 Td /F1 9.8 Tf  [(with support values, and then contracted all edges with less than 75% support. We generated 500 bootstrap replicates on all )] TJ ET
BT 26.250 170.325 Td /F1 9.8 Tf  [(datasets except for the two largest biological datasets, 16S.T and 16S.B.ALL, for which we used 346 and 573 bootstrap )] TJ ET
BT 26.250 158.420 Td /F1 9.8 Tf  [(replicates, respectively.)] TJ ET
BT 26.250 139.015 Td /F4 9.8 Tf  [(Table 1: Empirical statistics for reference alignments and reference trees for each dataset.)] TJ ET
BT 444.028 139.015 Td /F1 9.8 Tf  [( �# Taxa� is the number of )] TJ ET
BT 26.250 127.110 Td /F1 9.8 Tf  [(taxa. �# Sites� is the number of sites in the reference alignment, which is the curated alignment for the CRW datasets and the )] TJ ET
BT 26.250 115.206 Td /F1 9.8 Tf  [(true alignment for the Price 78K dataset. �Indels� is the percentage of cells in the reference alignment matrix that consist of )] TJ ET
BT 26.250 103.301 Td /F1 9.8 Tf  [(indels. �Res� is the resolution of the reference tree, or the percentage of internal edges present in the reference tree out of the )] TJ ET
BT 26.250 91.396 Td /F1 9.8 Tf  [(total possible number of edges. The p-distance between two sequences is the percentage of sites in which the two sequences )] TJ ET
BT 26.250 79.491 Td /F1 9.8 Tf  [(have different nucleotides, and is denoted by �p-dist�. �Avg p-dist� is the average p-distance across all pairs of sequences in the )] TJ ET
BT 26.250 67.587 Td /F1 9.8 Tf  [(reference alignment, and �Max p-dist� is the maximum p-distance across all pairs of sequences in the reference alignment. �Gap )] TJ ET
BT 26.250 55.682 Td /F1 9.8 Tf  [(Len� is the average length of a gap \(contiguous string of indels\) in the reference alignment. n=1 for all reported values.)] TJ ET
1.000 1.000 1.000 rg
26.250 44.301 555.000 1.500 re f
Q
q
15.000 44.301 577.500 732.699 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(that the selection of alignment method is very important to the systematics study.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(The main observation in this study is that only a small number of multiple sequence alignment methods can be run on datasets )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(with several thousand sequences. Furthermore, of those methods that can be run on large datasets, none produces alignments )] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(of sufficient accuracy to be useful in estimating highly accurate phylogenies. Therefore, when datasets are large and have )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(evolved with many indels, the input to species tree estimations \(i.e. either super-alignments or gene trees\) are likely to be of )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(poor accuracy; consequently, this suggests that species tree estimates will also have reduced accuracy for large datasets, )] TJ ET
BT 26.250 688.548 Td /F1 9.8 Tf  [(directly because of alignment difficulties.)] TJ ET
BT 26.250 651.945 Td /F4 12.0 Tf  [(Methodology)] TJ ET
BT 26.250 631.991 Td /F4 9.8 Tf  [(Overview)] TJ ET
BT 26.250 612.586 Td /F1 9.8 Tf  [(We used several rRNA biological datasets \(of up to 27,643 sequences\) and one simulated dataset \(of 78,132 sequences\) to )] TJ ET
BT 26.250 600.681 Td /F1 9.8 Tf  [(evaluate the alignment methods. The biological datasets have curated alignments based upon secondary structure and )] TJ ET
BT 26.250 588.777 Td /F1 9.8 Tf  [(reference trees produced by computing maximum likelihood trees with bootstrapping on each curated alignment, retaining only )] TJ ET
BT 26.250 576.872 Td /F1 9.8 Tf  [(the high support edges. For the simulated dataset, we have the true alignment and true tree. See Table 1 and the )] TJ ET
BT 26.250 564.967 Td /F1 9.8 Tf  [(supplementary online materials )] TJ ET
0.267 0.267 0.267 rg
BT 163.881 564.967 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 180.144 564.967 Td /F1 9.8 Tf  [( for details about these data.)] TJ ET
BT 26.250 545.562 Td /F1 9.8 Tf  [(For each dataset, we attempted to compute alignments using a collection of alignment methods, and for each alignment that we )] TJ ET
BT 26.250 533.658 Td /F1 9.8 Tf  [(generated, we computed a maximum likelihood tree using either RAxML or FastTree )] TJ ET
0.267 0.267 0.267 rg
BT 393.094 533.658 Td /F1 9.8 Tf  [([26] [27])] TJ ET
0.271 0.267 0.267 rg
BT 428.330 533.658 Td /F1 9.8 Tf  [(. We compared the estimated )] TJ ET
BT 26.250 521.753 Td /F1 9.8 Tf  [(alignments to the true or curated alignment to determine the alignment error rate, and we compared the estimated ML tree to )] TJ ET
BT 26.250 509.848 Td /F1 9.8 Tf  [(the true or reference tree to determine the tree error rate. We also recorded running time for each analysis.)] TJ ET
BT 26.250 490.443 Td /F4 9.8 Tf  [(Datasets)] TJ ET
BT 26.250 471.039 Td /F1 9.8 Tf  [(The biological datasets were drawn from Robin Gutell�s Comparative RNA Website \(CRW\) )] TJ ET
0.267 0.267 0.267 rg
BT 419.058 471.039 Td /F1 9.8 Tf  [([28])] TJ ET
0.271 0.267 0.267 rg
BT 435.321 471.039 Td /F1 9.8 Tf  [( and have curated alignments )] TJ ET
BT 26.250 459.134 Td /F1 9.8 Tf  [(based upon secondary structure. While secondary structure alignments are highly reliable, there is no guarantee that these are )] TJ ET
BT 26.250 447.229 Td /F1 9.8 Tf  [(perfectly correct. However, these are the most reliable benchmarks available to date for testing nucleotide alignment methods, )] TJ ET
BT 26.250 435.324 Td /F1 9.8 Tf  [(other than using simulated data. These biological datasets contain 16S and 23S sequences, markers that are frequently used )] TJ ET
BT 26.250 423.420 Td /F1 9.8 Tf  [(for estimating phylogenies. They range in size from about 100 sequences to almost 28,000 sequences. We used the )] TJ ET
BT 26.250 411.515 Td /F1 9.8 Tf  [(preprocessing steps in )] TJ ET
0.267 0.267 0.267 rg
BT 126.499 411.515 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 142.762 411.515 Td /F1 9.8 Tf  [( on these datasets to remove taxa that were more than 50% unsequenced, and to remove illegal )] TJ ET
BT 26.250 399.610 Td /F1 9.8 Tf  [(characters. The empirical statistics for the resulting curated alignments after preprocessing are listed in Table 1. Note that these )] TJ ET
BT 26.250 387.705 Td /F1 9.8 Tf  [(biological datasets are relatively �gappy�, with indels occupying 60-90% of the curated alignment matrix. They also have )] TJ ET
BT 26.250 375.801 Td /F1 9.8 Tf  [(different gap length distributions, and different average and maximum p-distances. Thus, these datasets have properties that )] TJ ET
BT 26.250 363.896 Td /F1 9.8 Tf  [(are challenging for alignment and phylogeny estimation, and are realistic examples of datasets used in large-scale phylogenetic )] TJ ET
BT 26.250 351.991 Td /F1 9.8 Tf  [(studies. See the Supplementary Materials online webpage )] TJ ET
0.267 0.267 0.267 rg
BT 280.413 351.991 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 296.676 351.991 Td /F1 9.8 Tf  [( for these data.)] TJ ET
BT 26.250 332.586 Td /F1 9.8 Tf  [(The simulated dataset was obtained from )] TJ ET
0.267 0.267 0.267 rg
BT 207.249 332.586 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 223.512 332.586 Td /F1 9.8 Tf  [(, with 78,132 DNA sequences and 1,287 sites in the true alignment. This dataset )] TJ ET
BT 26.250 320.682 Td /F1 9.8 Tf  [(is the last replicate from the simulation by )] TJ ET
0.267 0.267 0.267 rg
BT 207.775 320.682 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 224.038 320.682 Td /F1 9.8 Tf  [(, obtained at http://www.microbesonline.org/fasttree/; we call this the �Price 78K� )] TJ ET
BT 26.250 308.777 Td /F1 9.8 Tf  [(dataset. The empirical statistics for the true alignment on this dataset are in Table 1. Many of the empirical statistics for the )] TJ ET
BT 26.250 296.872 Td /F1 9.8 Tf  [(Price 78K dataset are similar to those of the empirical datasets; however, the Price 78K dataset has hardly any indels \(in fact )] TJ ET
BT 26.250 284.967 Td /F1 9.8 Tf  [(the gappiness is two orders of magnitude less than those exhibited in the biological datasets\) and the average gap length is )] TJ ET
BT 26.250 273.063 Td /F1 9.8 Tf  [(extremely short. As a result, the Price 78K dataset is potentially easier to align than the biological datasets. Because of its size, )] TJ ET
BT 26.250 261.158 Td /F1 9.8 Tf  [(however, the Price 78K dataset provides a test of scalability.)] TJ ET
BT 26.250 241.753 Td /F1 9.8 Tf  [(Reference alignments and trees were computed as follows. For the Price 78K dataset, we used the true alignment as the )] TJ ET
BT 26.250 229.848 Td /F1 9.8 Tf  [(reference alignment, and the true tree as the reference tree; these are known because the Price 78K dataset is simulated. For )] TJ ET
BT 26.250 217.944 Td /F1 9.8 Tf  [(the biological datasets, the curated alignment, modified by our minor cleaning operations, is the reference alignment. We )] TJ ET
BT 26.250 206.039 Td /F1 9.8 Tf  [(computed unaligned sequences from the reference alignments by simply deleting indels \(�-�\). To obtain reference trees for the )] TJ ET
BT 26.250 194.134 Td /F1 9.8 Tf  [(biological datasets, we performed rapid bootstrapping analyses with RAxML )] TJ ET
0.267 0.267 0.267 rg
BT 356.258 194.134 Td /F1 9.8 Tf  [([29])] TJ ET
0.271 0.267 0.267 rg
BT 372.521 194.134 Td /F1 9.8 Tf  [( on the curated alignment to produce a tree )] TJ ET
BT 26.250 182.229 Td /F1 9.8 Tf  [(with support values, and then contracted all edges with less than 75% support. We generated 500 bootstrap replicates on all )] TJ ET
BT 26.250 170.325 Td /F1 9.8 Tf  [(datasets except for the two largest biological datasets, 16S.T and 16S.B.ALL, for which we used 346 and 573 bootstrap )] TJ ET
BT 26.250 158.420 Td /F1 9.8 Tf  [(replicates, respectively.)] TJ ET
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BT 31.875 655.358 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
132.427 665.212 61.658 0.750 re f
132.427 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 655.358 Td /F1 9.8 Tf  [(278)] TJ ET
0.267 0.267 0.267 rg
193.335 665.212 61.044 0.750 re f
193.335 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 655.358 Td /F1 9.8 Tf  [(10738)] TJ ET
0.267 0.267 0.267 rg
253.630 665.212 60.459 0.750 re f
253.630 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 655.358 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
313.339 665.212 63.255 0.750 re f
313.339 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 655.358 Td /F1 9.8 Tf  [(37.7)] TJ ET
0.267 0.267 0.267 rg
375.844 665.212 68.983 0.750 re f
375.844 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 655.358 Td /F1 9.8 Tf  [(70.3)] TJ ET
0.267 0.267 0.267 rg
444.076 665.212 70.027 0.750 re f
444.076 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 655.358 Td /F1 9.8 Tf  [(83.7)] TJ ET
0.267 0.267 0.267 rg
513.353 665.212 67.522 0.750 re f
513.353 649.331 0.750 16.631 re f
580.125 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 655.358 Td /F1 9.8 Tf  [(31.9)] TJ ET
0.267 0.267 0.267 rg
26.625 649.331 106.552 0.750 re f
26.625 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 639.476 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 649.331 61.658 0.750 re f
132.427 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 639.476 Td /F1 9.8 Tf  [(263)] TJ ET
0.267 0.267 0.267 rg
193.335 649.331 61.044 0.750 re f
193.335 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 639.476 Td /F1 9.8 Tf  [(10305)] TJ ET
0.267 0.267 0.267 rg
253.630 649.331 60.459 0.750 re f
253.630 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 639.476 Td /F1 9.8 Tf  [(60.0)] TJ ET
0.267 0.267 0.267 rg
313.339 649.331 63.255 0.750 re f
313.339 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 639.476 Td /F1 9.8 Tf  [(37.7)] TJ ET
0.267 0.267 0.267 rg
375.844 649.331 68.983 0.750 re f
375.844 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 639.476 Td /F1 9.8 Tf  [(70.7)] TJ ET
0.267 0.267 0.267 rg
444.076 649.331 70.027 0.750 re f
444.076 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 639.476 Td /F1 9.8 Tf  [(83.5)] TJ ET
0.267 0.267 0.267 rg
513.353 649.331 67.522 0.750 re f
513.353 633.450 0.750 16.631 re f
580.125 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 639.476 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
26.625 633.450 106.552 0.750 re f
26.625 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 623.595 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 633.450 61.658 0.750 re f
132.427 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 623.595 Td /F1 9.8 Tf  [(144)] TJ ET
0.267 0.267 0.267 rg
193.335 633.450 61.044 0.750 re f
193.335 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 623.595 Td /F1 9.8 Tf  [(8619)] TJ ET
0.267 0.267 0.267 rg
253.630 633.450 60.459 0.750 re f
253.630 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 623.595 Td /F1 9.8 Tf  [(64.5)] TJ ET
0.267 0.267 0.267 rg
313.339 633.450 63.255 0.750 re f
313.339 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 623.595 Td /F1 9.8 Tf  [(30.3)] TJ ET
0.267 0.267 0.267 rg
375.844 633.450 68.983 0.750 re f
375.844 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 623.595 Td /F1 9.8 Tf  [(57.0)] TJ ET
0.267 0.267 0.267 rg
444.076 633.450 70.027 0.750 re f
444.076 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 623.595 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
513.353 633.450 67.522 0.750 re f
513.353 617.569 0.750 16.631 re f
580.125 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 623.595 Td /F1 9.8 Tf  [(13.5)] TJ ET
0.267 0.267 0.267 rg
26.625 617.569 106.552 0.750 re f
26.625 601.688 106.552 0.750 re f
26.625 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 607.714 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
132.427 617.569 61.658 0.750 re f
132.427 601.688 61.658 0.750 re f
132.427 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 607.714 Td /F1 9.8 Tf  [(117)] TJ ET
0.267 0.267 0.267 rg
193.335 617.569 61.044 0.750 re f
193.335 601.688 61.044 0.750 re f
193.335 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 607.714 Td /F1 9.8 Tf  [(9079)] TJ ET
0.267 0.267 0.267 rg
253.630 617.569 60.459 0.750 re f
253.630 601.688 60.459 0.750 re f
253.630 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 607.714 Td /F1 9.8 Tf  [(65.8)] TJ ET
0.267 0.267 0.267 rg
313.339 617.569 63.255 0.750 re f
313.339 601.688 63.255 0.750 re f
313.339 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 607.714 Td /F1 9.8 Tf  [(29.6)] TJ ET
0.267 0.267 0.267 rg
375.844 617.569 68.983 0.750 re f
375.844 601.688 68.983 0.750 re f
375.844 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 607.714 Td /F1 9.8 Tf  [(51.7)] TJ ET
0.267 0.267 0.267 rg
444.076 617.569 70.027 0.750 re f
444.076 601.688 70.027 0.750 re f
444.076 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 607.714 Td /F1 9.8 Tf  [(59.7)] TJ ET
0.267 0.267 0.267 rg
513.353 617.569 67.522 0.750 re f
513.353 601.688 67.522 0.750 re f
513.353 601.688 0.750 16.631 re f
580.125 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 607.714 Td /F1 9.8 Tf  [(12.6)] TJ ET
BT 26.250 537.091 Td /F4 12.0 Tf  [(Methods)] TJ ET
BT 26.250 517.137 Td /F4 9.8 Tf  [(Alignment methods)] TJ ET
BT 26.250 497.732 Td /F1 9.8 Tf  [(We estimated alignments using SAT�, Prank+GT )] TJ ET
0.267 0.267 0.267 rg
BT 241.647 497.732 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 257.910 497.732 Td /F1 9.8 Tf  [(, Muscle, Opal, MAFFT, MAFFT-PartTree )] TJ ET
0.267 0.267 0.267 rg
BT 439.942 497.732 Td /F1 9.8 Tf  [([30])] TJ ET
0.271 0.267 0.267 rg
BT 456.205 497.732 Td /F1 9.8 Tf  [(, ClustalW, and ClustalW-)] TJ ET
BT 26.250 485.827 Td /F1 9.8 Tf  [(Quicktree. The MAFFT-PartTree and ClustalW-Quicktree, methods are the variants of MAFFT and ClustalW, respectively, )] TJ ET
BT 26.250 473.922 Td /F1 9.8 Tf  [(designed for use on very large datasets. The commands used for these methods are provided in the Appendix. Due to )] TJ ET
BT 26.250 462.018 Td /F1 9.8 Tf  [(computational challenges, not all alignment methods could be run on all datasets; details of this are given in Results below.)] TJ ET
BT 26.250 442.613 Td /F1 9.8 Tf  [(The SAT� analysis we performed depended on the dataset size. The default setting for SAT� was used on the six smallest )] TJ ET
BT 26.250 430.708 Td /F1 9.8 Tf  [(datasets. The default version begins by computing four trees, formed by running RAxML to completion on MAFFT, Prank+GT )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 418.803 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 42.513 418.803 Td /F1 9.8 Tf  [(, Muscle, and ClustalW alignments. It then takes the tree/alignment pair that had the best ML score as its starting tree, and )] TJ ET
BT 26.250 406.899 Td /F1 9.8 Tf  [(iterates, alternating between alignment estimation \(using a divide-and-conquer technique that constructs alignments on subsets )] TJ ET
BT 26.250 394.994 Td /F1 9.8 Tf  [(of taxa using MAFFT, and then merges alignments using Muscle or Opal\) and tree estimation using RAxML. This iterative stage )] TJ ET
BT 26.250 383.089 Td /F1 9.8 Tf  [(lasts by default for 24 hours. The running time of SAT� thus includes a very expensive initial stage where four different two-)] TJ ET
BT 26.250 371.184 Td /F1 9.8 Tf  [(phase methods are run, and a potentially expensive second stage if the number of iterations that are run is large.)] TJ ET
BT 26.250 351.780 Td /F1 9.8 Tf  [(We modified this default setting for the four larger datasets, as follows. First, we replaced the expensive initial stage by only )] TJ ET
BT 26.250 339.875 Td /F1 9.8 Tf  [(computing RAxML on the MAFFT-PartTree alignment. Second, instead of running the next stage for 24 hours, we set the )] TJ ET
BT 26.250 327.970 Td /F1 9.8 Tf  [(number of iterations in advance. On the 16S.3 dataset we ran SAT� for five iterations, and we ran SAT� for ten iterations on the )] TJ ET
BT 26.250 316.065 Td /F1 9.8 Tf  [(16S.T dataset. We attempted to run SAT� on the largest biological dataset \(16S.B.ALL, with 27,643 sequences\), but it failed to )] TJ ET
BT 26.250 304.161 Td /F1 9.8 Tf  [(complete its first iteration. We therefore did not attempt to run SAT� on the largest dataset \(the Price 78K dataset\).)] TJ ET
BT 26.250 284.756 Td /F4 9.8 Tf  [(Maximum Likelihood Estimation Methods)] TJ ET
BT 26.250 265.351 Td /F1 9.8 Tf  [(We ran RAxML to compute trees on all but the Price 78K dataset, but tailored the specific RAxML command according to the )] TJ ET
BT 26.250 253.446 Td /F1 9.8 Tf  [(dataset size; see the Appendix for details. For the Price 78K dataset, we computed the ML tree using FastTree, since our other )] TJ ET
BT 26.250 241.542 Td /F1 9.8 Tf  [(analyses suggested that the RAxML analysis would require many months to complete.)] TJ ET
BT 26.250 222.137 Td /F4 9.8 Tf  [(Measurements)] TJ ET
BT 26.250 202.732 Td /F1 9.8 Tf  [(For each alignment produced on each dataset, we used custom code )] TJ ET
0.267 0.267 0.267 rg
BT 327.574 202.732 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 343.837 202.732 Td /F1 9.8 Tf  [( to compute the alignment error using the SP-FN error )] TJ ET
BT 26.250 190.827 Td /F1 9.8 Tf  [(measure, which is the proportion of the truly homologous pairs of nucleotides \(as defined by the reference alignment\) that are )] TJ ET
BT 26.250 178.923 Td /F1 9.8 Tf  [(missing in the estimated alignment )] TJ ET
0.267 0.267 0.267 rg
BT 178.516 178.923 Td /F1 9.8 Tf  [([31])] TJ ET
0.271 0.267 0.267 rg
BT 194.779 178.923 Td /F1 9.8 Tf  [(. For each tree produced on each alignment, we used custom code )] TJ ET
0.267 0.267 0.267 rg
BT 486.343 178.923 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 502.606 178.923 Td /F1 9.8 Tf  [( to compute the )] TJ ET
BT 26.250 167.018 Td /F1 9.8 Tf  [(missing branch \(or false negative\) rate, which is the proportion of the internal branches in the reference tree missing in the )] TJ ET
BT 26.250 155.113 Td /F1 9.8 Tf  [(estimated tree. We use the missing branch rate instead of the bipartition distance \(also known as the Robinson-Foulds \(RF\) )] TJ ET
BT 26.250 143.208 Td /F1 9.8 Tf  [(error rate )] TJ ET
0.267 0.267 0.267 rg
BT 69.053 143.208 Td /F1 9.8 Tf  [([32])] TJ ET
0.271 0.267 0.267 rg
BT 85.316 143.208 Td /F1 9.8 Tf  [(\) because the biological reference trees are not completely resolved \(high RF rates are always obtained when the )] TJ ET
BT 26.250 131.304 Td /F1 9.8 Tf  [(reference trees are highly unresolved\).)] TJ ET
BT 26.250 111.899 Td /F1 9.8 Tf  [(We also recorded the running time and the memory requirement. For the running time, we report the clock time; this is )] TJ ET
BT 26.250 99.994 Td /F1 9.8 Tf  [(approximate, since analyses were performed on machines that were not dedicated to these analyses. For the memory )] TJ ET
BT 26.250 88.089 Td /F1 9.8 Tf  [(requirement, we only report the memory available in the machine on which the method was able to run.)] TJ ET
BT 26.250 51.487 Td /F4 12.0 Tf  [(Results)] TJ ET
Q
q
15.000 21.652 577.500 755.348 re W n
1.000 1.000 1.000 rg
26.250 601.312 555.000 175.687 re f
0.267 0.267 0.267 rg
26.625 776.625 106.552 0.750 re f
26.625 760.500 0.750 16.875 re f
132.427 776.625 61.658 0.750 re f
132.427 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 137.677 766.770 Td /F4 9.8 Tf  [(# Taxa)] TJ ET
0.267 0.267 0.267 rg
193.335 776.625 61.044 0.750 re f
193.335 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 198.585 766.770 Td /F4 9.8 Tf  [(# Cols)] TJ ET
0.267 0.267 0.267 rg
253.630 776.625 60.459 0.750 re f
253.630 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 258.880 766.770 Td /F4 9.8 Tf  [(Res \(%\))] TJ ET
0.267 0.267 0.267 rg
313.339 776.625 63.255 0.750 re f
313.339 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 318.589 766.770 Td /F4 9.8 Tf  [(Avg p-dist)] TJ ET
0.267 0.267 0.267 rg
375.844 776.625 68.983 0.750 re f
375.844 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 381.094 766.770 Td /F4 9.8 Tf  [(Max p-dist)] TJ ET
0.267 0.267 0.267 rg
444.076 776.625 70.027 0.750 re f
444.076 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 449.326 766.770 Td /F4 9.8 Tf  [(Indels \(%\))] TJ ET
0.267 0.267 0.267 rg
513.353 776.625 67.522 0.750 re f
513.353 760.500 0.750 16.875 re f
580.125 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 518.603 766.770 Td /F4 9.8 Tf  [(Avg gap )] TJ ET
BT 559.777 766.770 Td /F4 9.8 Tf  [(len)] TJ ET
0.267 0.267 0.267 rg
26.625 760.500 106.552 0.750 re f
26.625 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 750.645 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
132.427 760.500 61.658 0.750 re f
132.427 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 750.645 Td /F1 9.8 Tf  [(78132)] TJ ET
0.267 0.267 0.267 rg
193.335 760.500 61.044 0.750 re f
193.335 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 750.645 Td /F1 9.8 Tf  [(1287)] TJ ET
0.267 0.267 0.267 rg
253.630 760.500 60.459 0.750 re f
253.630 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 750.645 Td /F1 9.8 Tf  [(100.0)] TJ ET
0.267 0.267 0.267 rg
313.339 760.500 63.255 0.750 re f
313.339 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 750.645 Td /F1 9.8 Tf  [(40.6)] TJ ET
0.267 0.267 0.267 rg
375.844 760.500 68.983 0.750 re f
375.844 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 750.645 Td /F1 9.8 Tf  [(64.0)] TJ ET
0.267 0.267 0.267 rg
444.076 760.500 70.027 0.750 re f
444.076 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 750.645 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
513.353 760.500 67.522 0.750 re f
513.353 744.619 0.750 16.631 re f
580.125 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 750.645 Td /F1 9.8 Tf  [(1.3)] TJ ET
0.267 0.267 0.267 rg
26.625 744.619 106.552 0.750 re f
26.625 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 734.764 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
132.427 744.619 61.658 0.750 re f
132.427 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 734.764 Td /F1 9.8 Tf  [(27643)] TJ ET
0.267 0.267 0.267 rg
193.335 744.619 61.044 0.750 re f
193.335 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 734.764 Td /F1 9.8 Tf  [(6857)] TJ ET
0.267 0.267 0.267 rg
253.630 744.619 60.459 0.750 re f
253.630 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 734.764 Td /F1 9.8 Tf  [(17.4)] TJ ET
0.267 0.267 0.267 rg
313.339 744.619 63.255 0.750 re f
313.339 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 734.764 Td /F1 9.8 Tf  [(21.0)] TJ ET
0.267 0.267 0.267 rg
375.844 744.619 68.983 0.750 re f
375.844 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 734.764 Td /F1 9.8 Tf  [(76.9)] TJ ET
0.267 0.267 0.267 rg
444.076 744.619 70.027 0.750 re f
444.076 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 734.764 Td /F1 9.8 Tf  [(80.0)] TJ ET
0.267 0.267 0.267 rg
513.353 744.619 67.522 0.750 re f
513.353 728.737 0.750 16.631 re f
580.125 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 734.764 Td /F1 9.8 Tf  [(4.9)] TJ ET
0.267 0.267 0.267 rg
26.625 728.737 106.552 0.750 re f
26.625 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 718.883 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
132.427 728.737 61.658 0.750 re f
132.427 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 718.883 Td /F1 9.8 Tf  [(7350)] TJ ET
0.267 0.267 0.267 rg
193.335 728.737 61.044 0.750 re f
193.335 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 718.883 Td /F1 9.8 Tf  [(11856)] TJ ET
0.267 0.267 0.267 rg
253.630 728.737 60.459 0.750 re f
253.630 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 718.883 Td /F1 9.8 Tf  [(49.9)] TJ ET
0.267 0.267 0.267 rg
313.339 728.737 63.255 0.750 re f
313.339 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 718.883 Td /F1 9.8 Tf  [(34.5)] TJ ET
0.267 0.267 0.267 rg
375.844 728.737 68.983 0.750 re f
375.844 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 718.883 Td /F1 9.8 Tf  [(90.1)] TJ ET
0.267 0.267 0.267 rg
444.076 728.737 70.027 0.750 re f
444.076 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 718.883 Td /F1 9.8 Tf  [(87.4)] TJ ET
0.267 0.267 0.267 rg
513.353 728.737 67.522 0.750 re f
513.353 712.856 0.750 16.631 re f
580.125 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 718.883 Td /F1 9.8 Tf  [(12.1)] TJ ET
0.267 0.267 0.267 rg
26.625 712.856 106.552 0.750 re f
26.625 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 703.001 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
132.427 712.856 61.658 0.750 re f
132.427 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 703.001 Td /F1 9.8 Tf  [(6323)] TJ ET
0.267 0.267 0.267 rg
193.335 712.856 61.044 0.750 re f
193.335 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 703.001 Td /F1 9.8 Tf  [(8716)] TJ ET
0.267 0.267 0.267 rg
253.630 712.856 60.459 0.750 re f
253.630 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 703.001 Td /F1 9.8 Tf  [(50.4)] TJ ET
0.267 0.267 0.267 rg
313.339 712.856 63.255 0.750 re f
313.339 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 703.001 Td /F1 9.8 Tf  [(31.5)] TJ ET
0.267 0.267 0.267 rg
375.844 712.856 68.983 0.750 re f
375.844 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 703.001 Td /F1 9.8 Tf  [(83.3)] TJ ET
0.267 0.267 0.267 rg
444.076 712.856 70.027 0.750 re f
444.076 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 703.001 Td /F1 9.8 Tf  [(82.1)] TJ ET
0.267 0.267 0.267 rg
513.353 712.856 67.522 0.750 re f
513.353 696.975 0.750 16.631 re f
580.125 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 703.001 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
26.625 696.975 106.552 0.750 re f
26.625 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 687.120 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 696.975 61.658 0.750 re f
132.427 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 687.120 Td /F1 9.8 Tf  [(1028)] TJ ET
0.267 0.267 0.267 rg
193.335 696.975 61.044 0.750 re f
193.335 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 687.120 Td /F1 9.8 Tf  [(4907)] TJ ET
0.267 0.267 0.267 rg
253.630 696.975 60.459 0.750 re f
253.630 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 687.120 Td /F1 9.8 Tf  [(42.2)] TJ ET
0.267 0.267 0.267 rg
313.339 696.975 63.255 0.750 re f
313.339 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 687.120 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
375.844 696.975 68.983 0.750 re f
375.844 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 687.120 Td /F1 9.8 Tf  [(100.0)] TJ ET
0.267 0.267 0.267 rg
444.076 696.975 70.027 0.750 re f
444.076 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 687.120 Td /F1 9.8 Tf  [(82.6)] TJ ET
0.267 0.267 0.267 rg
513.353 696.975 67.522 0.750 re f
513.353 681.094 0.750 16.631 re f
580.125 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 687.120 Td /F1 9.8 Tf  [(22.0)] TJ ET
0.267 0.267 0.267 rg
26.625 681.094 106.552 0.750 re f
26.625 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 671.239 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
132.427 681.094 61.658 0.750 re f
132.427 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 671.239 Td /F1 9.8 Tf  [(901)] TJ ET
0.267 0.267 0.267 rg
193.335 681.094 61.044 0.750 re f
193.335 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 671.239 Td /F1 9.8 Tf  [(4722)] TJ ET
0.267 0.267 0.267 rg
253.630 681.094 60.459 0.750 re f
253.630 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 671.239 Td /F1 9.8 Tf  [(46.9)] TJ ET
0.267 0.267 0.267 rg
313.339 681.094 63.255 0.750 re f
313.339 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 671.239 Td /F1 9.8 Tf  [(35.9)] TJ ET
0.267 0.267 0.267 rg
375.844 681.094 68.983 0.750 re f
375.844 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 671.239 Td /F1 9.8 Tf  [(88.7)] TJ ET
0.267 0.267 0.267 rg
444.076 681.094 70.027 0.750 re f
444.076 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 671.239 Td /F1 9.8 Tf  [(78.1)] TJ ET
0.267 0.267 0.267 rg
513.353 681.094 67.522 0.750 re f
513.353 665.212 0.750 16.631 re f
580.125 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 671.239 Td /F1 9.8 Tf  [(17.2)] TJ ET
0.267 0.267 0.267 rg
26.625 665.212 106.552 0.750 re f
26.625 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 655.358 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
132.427 665.212 61.658 0.750 re f
132.427 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 655.358 Td /F1 9.8 Tf  [(278)] TJ ET
0.267 0.267 0.267 rg
193.335 665.212 61.044 0.750 re f
193.335 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 655.358 Td /F1 9.8 Tf  [(10738)] TJ ET
0.267 0.267 0.267 rg
253.630 665.212 60.459 0.750 re f
253.630 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 655.358 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
313.339 665.212 63.255 0.750 re f
313.339 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 655.358 Td /F1 9.8 Tf  [(37.7)] TJ ET
0.267 0.267 0.267 rg
375.844 665.212 68.983 0.750 re f
375.844 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 655.358 Td /F1 9.8 Tf  [(70.3)] TJ ET
0.267 0.267 0.267 rg
444.076 665.212 70.027 0.750 re f
444.076 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 655.358 Td /F1 9.8 Tf  [(83.7)] TJ ET
0.267 0.267 0.267 rg
513.353 665.212 67.522 0.750 re f
513.353 649.331 0.750 16.631 re f
580.125 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 655.358 Td /F1 9.8 Tf  [(31.9)] TJ ET
0.267 0.267 0.267 rg
26.625 649.331 106.552 0.750 re f
26.625 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 639.476 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 649.331 61.658 0.750 re f
132.427 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 639.476 Td /F1 9.8 Tf  [(263)] TJ ET
0.267 0.267 0.267 rg
193.335 649.331 61.044 0.750 re f
193.335 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 639.476 Td /F1 9.8 Tf  [(10305)] TJ ET
0.267 0.267 0.267 rg
253.630 649.331 60.459 0.750 re f
253.630 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 639.476 Td /F1 9.8 Tf  [(60.0)] TJ ET
0.267 0.267 0.267 rg
313.339 649.331 63.255 0.750 re f
313.339 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 639.476 Td /F1 9.8 Tf  [(37.7)] TJ ET
0.267 0.267 0.267 rg
375.844 649.331 68.983 0.750 re f
375.844 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 639.476 Td /F1 9.8 Tf  [(70.7)] TJ ET
0.267 0.267 0.267 rg
444.076 649.331 70.027 0.750 re f
444.076 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 639.476 Td /F1 9.8 Tf  [(83.5)] TJ ET
0.267 0.267 0.267 rg
513.353 649.331 67.522 0.750 re f
513.353 633.450 0.750 16.631 re f
580.125 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 639.476 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
26.625 633.450 106.552 0.750 re f
26.625 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 623.595 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 633.450 61.658 0.750 re f
132.427 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 623.595 Td /F1 9.8 Tf  [(144)] TJ ET
0.267 0.267 0.267 rg
193.335 633.450 61.044 0.750 re f
193.335 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 623.595 Td /F1 9.8 Tf  [(8619)] TJ ET
0.267 0.267 0.267 rg
253.630 633.450 60.459 0.750 re f
253.630 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 623.595 Td /F1 9.8 Tf  [(64.5)] TJ ET
0.267 0.267 0.267 rg
313.339 633.450 63.255 0.750 re f
313.339 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 623.595 Td /F1 9.8 Tf  [(30.3)] TJ ET
0.267 0.267 0.267 rg
375.844 633.450 68.983 0.750 re f
375.844 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 623.595 Td /F1 9.8 Tf  [(57.0)] TJ ET
0.267 0.267 0.267 rg
444.076 633.450 70.027 0.750 re f
444.076 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 623.595 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
513.353 633.450 67.522 0.750 re f
513.353 617.569 0.750 16.631 re f
580.125 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 623.595 Td /F1 9.8 Tf  [(13.5)] TJ ET
0.267 0.267 0.267 rg
26.625 617.569 106.552 0.750 re f
26.625 601.688 106.552 0.750 re f
26.625 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 607.714 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
132.427 617.569 61.658 0.750 re f
132.427 601.688 61.658 0.750 re f
132.427 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 607.714 Td /F1 9.8 Tf  [(117)] TJ ET
0.267 0.267 0.267 rg
193.335 617.569 61.044 0.750 re f
193.335 601.688 61.044 0.750 re f
193.335 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 607.714 Td /F1 9.8 Tf  [(9079)] TJ ET
0.267 0.267 0.267 rg
253.630 617.569 60.459 0.750 re f
253.630 601.688 60.459 0.750 re f
253.630 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 607.714 Td /F1 9.8 Tf  [(65.8)] TJ ET
0.267 0.267 0.267 rg
313.339 617.569 63.255 0.750 re f
313.339 601.688 63.255 0.750 re f
313.339 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 607.714 Td /F1 9.8 Tf  [(29.6)] TJ ET
0.267 0.267 0.267 rg
375.844 617.569 68.983 0.750 re f
375.844 601.688 68.983 0.750 re f
375.844 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 607.714 Td /F1 9.8 Tf  [(51.7)] TJ ET
0.267 0.267 0.267 rg
444.076 617.569 70.027 0.750 re f
444.076 601.688 70.027 0.750 re f
444.076 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 607.714 Td /F1 9.8 Tf  [(59.7)] TJ ET
0.267 0.267 0.267 rg
513.353 617.569 67.522 0.750 re f
513.353 601.688 67.522 0.750 re f
513.353 601.688 0.750 16.631 re f
580.125 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 607.714 Td /F1 9.8 Tf  [(12.6)] TJ ET
BT 26.250 537.091 Td /F4 12.0 Tf  [(Methods)] TJ ET
BT 26.250 517.137 Td /F4 9.8 Tf  [(Alignment methods)] TJ ET
BT 26.250 497.732 Td /F1 9.8 Tf  [(We estimated alignments using SAT�, Prank+GT )] TJ ET
0.267 0.267 0.267 rg
BT 241.647 497.732 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 257.910 497.732 Td /F1 9.8 Tf  [(, Muscle, Opal, MAFFT, MAFFT-PartTree )] TJ ET
0.267 0.267 0.267 rg
BT 439.942 497.732 Td /F1 9.8 Tf  [([30])] TJ ET
0.271 0.267 0.267 rg
BT 456.205 497.732 Td /F1 9.8 Tf  [(, ClustalW, and ClustalW-)] TJ ET
BT 26.250 485.827 Td /F1 9.8 Tf  [(Quicktree. The MAFFT-PartTree and ClustalW-Quicktree, methods are the variants of MAFFT and ClustalW, respectively, )] TJ ET
BT 26.250 473.922 Td /F1 9.8 Tf  [(designed for use on very large datasets. The commands used for these methods are provided in the Appendix. Due to )] TJ ET
BT 26.250 462.018 Td /F1 9.8 Tf  [(computational challenges, not all alignment methods could be run on all datasets; details of this are given in Results below.)] TJ ET
BT 26.250 442.613 Td /F1 9.8 Tf  [(The SAT� analysis we performed depended on the dataset size. The default setting for SAT� was used on the six smallest )] TJ ET
BT 26.250 430.708 Td /F1 9.8 Tf  [(datasets. The default version begins by computing four trees, formed by running RAxML to completion on MAFFT, Prank+GT )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 418.803 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 42.513 418.803 Td /F1 9.8 Tf  [(, Muscle, and ClustalW alignments. It then takes the tree/alignment pair that had the best ML score as its starting tree, and )] TJ ET
BT 26.250 406.899 Td /F1 9.8 Tf  [(iterates, alternating between alignment estimation \(using a divide-and-conquer technique that constructs alignments on subsets )] TJ ET
BT 26.250 394.994 Td /F1 9.8 Tf  [(of taxa using MAFFT, and then merges alignments using Muscle or Opal\) and tree estimation using RAxML. This iterative stage )] TJ ET
BT 26.250 383.089 Td /F1 9.8 Tf  [(lasts by default for 24 hours. The running time of SAT� thus includes a very expensive initial stage where four different two-)] TJ ET
BT 26.250 371.184 Td /F1 9.8 Tf  [(phase methods are run, and a potentially expensive second stage if the number of iterations that are run is large.)] TJ ET
BT 26.250 351.780 Td /F1 9.8 Tf  [(We modified this default setting for the four larger datasets, as follows. First, we replaced the expensive initial stage by only )] TJ ET
BT 26.250 339.875 Td /F1 9.8 Tf  [(computing RAxML on the MAFFT-PartTree alignment. Second, instead of running the next stage for 24 hours, we set the )] TJ ET
BT 26.250 327.970 Td /F1 9.8 Tf  [(number of iterations in advance. On the 16S.3 dataset we ran SAT� for five iterations, and we ran SAT� for ten iterations on the )] TJ ET
BT 26.250 316.065 Td /F1 9.8 Tf  [(16S.T dataset. We attempted to run SAT� on the largest biological dataset \(16S.B.ALL, with 27,643 sequences\), but it failed to )] TJ ET
BT 26.250 304.161 Td /F1 9.8 Tf  [(complete its first iteration. We therefore did not attempt to run SAT� on the largest dataset \(the Price 78K dataset\).)] TJ ET
BT 26.250 284.756 Td /F4 9.8 Tf  [(Maximum Likelihood Estimation Methods)] TJ ET
BT 26.250 265.351 Td /F1 9.8 Tf  [(We ran RAxML to compute trees on all but the Price 78K dataset, but tailored the specific RAxML command according to the )] TJ ET
BT 26.250 253.446 Td /F1 9.8 Tf  [(dataset size; see the Appendix for details. For the Price 78K dataset, we computed the ML tree using FastTree, since our other )] TJ ET
BT 26.250 241.542 Td /F1 9.8 Tf  [(analyses suggested that the RAxML analysis would require many months to complete.)] TJ ET
BT 26.250 222.137 Td /F4 9.8 Tf  [(Measurements)] TJ ET
BT 26.250 202.732 Td /F1 9.8 Tf  [(For each alignment produced on each dataset, we used custom code )] TJ ET
0.267 0.267 0.267 rg
BT 327.574 202.732 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 343.837 202.732 Td /F1 9.8 Tf  [( to compute the alignment error using the SP-FN error )] TJ ET
BT 26.250 190.827 Td /F1 9.8 Tf  [(measure, which is the proportion of the truly homologous pairs of nucleotides \(as defined by the reference alignment\) that are )] TJ ET
BT 26.250 178.923 Td /F1 9.8 Tf  [(missing in the estimated alignment )] TJ ET
0.267 0.267 0.267 rg
BT 178.516 178.923 Td /F1 9.8 Tf  [([31])] TJ ET
0.271 0.267 0.267 rg
BT 194.779 178.923 Td /F1 9.8 Tf  [(. For each tree produced on each alignment, we used custom code )] TJ ET
0.267 0.267 0.267 rg
BT 486.343 178.923 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 502.606 178.923 Td /F1 9.8 Tf  [( to compute the )] TJ ET
BT 26.250 167.018 Td /F1 9.8 Tf  [(missing branch \(or false negative\) rate, which is the proportion of the internal branches in the reference tree missing in the )] TJ ET
BT 26.250 155.113 Td /F1 9.8 Tf  [(estimated tree. We use the missing branch rate instead of the bipartition distance \(also known as the Robinson-Foulds \(RF\) )] TJ ET
BT 26.250 143.208 Td /F1 9.8 Tf  [(error rate )] TJ ET
0.267 0.267 0.267 rg
BT 69.053 143.208 Td /F1 9.8 Tf  [([32])] TJ ET
0.271 0.267 0.267 rg
BT 85.316 143.208 Td /F1 9.8 Tf  [(\) because the biological reference trees are not completely resolved \(high RF rates are always obtained when the )] TJ ET
BT 26.250 131.304 Td /F1 9.8 Tf  [(reference trees are highly unresolved\).)] TJ ET
BT 26.250 111.899 Td /F1 9.8 Tf  [(We also recorded the running time and the memory requirement. For the running time, we report the clock time; this is )] TJ ET
BT 26.250 99.994 Td /F1 9.8 Tf  [(approximate, since analyses were performed on machines that were not dedicated to these analyses. For the memory )] TJ ET
BT 26.250 88.089 Td /F1 9.8 Tf  [(requirement, we only report the memory available in the machine on which the method was able to run.)] TJ ET
BT 26.250 51.487 Td /F4 12.0 Tf  [(Results)] TJ ET
Q
q
15.000 21.652 577.500 755.348 re W n
1.000 1.000 1.000 rg
26.250 601.312 555.000 175.687 re f
0.267 0.267 0.267 rg
26.625 776.625 106.552 0.750 re f
26.625 760.500 0.750 16.875 re f
132.427 776.625 61.658 0.750 re f
132.427 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 137.677 766.770 Td /F4 9.8 Tf  [(# Taxa)] TJ ET
0.267 0.267 0.267 rg
193.335 776.625 61.044 0.750 re f
193.335 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 198.585 766.770 Td /F4 9.8 Tf  [(# Cols)] TJ ET
0.267 0.267 0.267 rg
253.630 776.625 60.459 0.750 re f
253.630 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 258.880 766.770 Td /F4 9.8 Tf  [(Res \(%\))] TJ ET
0.267 0.267 0.267 rg
313.339 776.625 63.255 0.750 re f
313.339 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 318.589 766.770 Td /F4 9.8 Tf  [(Avg p-dist)] TJ ET
0.267 0.267 0.267 rg
375.844 776.625 68.983 0.750 re f
375.844 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 381.094 766.770 Td /F4 9.8 Tf  [(Max p-dist)] TJ ET
0.267 0.267 0.267 rg
444.076 776.625 70.027 0.750 re f
444.076 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 449.326 766.770 Td /F4 9.8 Tf  [(Indels \(%\))] TJ ET
0.267 0.267 0.267 rg
513.353 776.625 67.522 0.750 re f
513.353 760.500 0.750 16.875 re f
580.125 760.500 0.750 16.875 re f
0.271 0.267 0.267 rg
BT 518.603 766.770 Td /F4 9.8 Tf  [(Avg gap )] TJ ET
BT 559.777 766.770 Td /F4 9.8 Tf  [(len)] TJ ET
0.267 0.267 0.267 rg
26.625 760.500 106.552 0.750 re f
26.625 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 750.645 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
132.427 760.500 61.658 0.750 re f
132.427 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 750.645 Td /F1 9.8 Tf  [(78132)] TJ ET
0.267 0.267 0.267 rg
193.335 760.500 61.044 0.750 re f
193.335 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 750.645 Td /F1 9.8 Tf  [(1287)] TJ ET
0.267 0.267 0.267 rg
253.630 760.500 60.459 0.750 re f
253.630 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 750.645 Td /F1 9.8 Tf  [(100.0)] TJ ET
0.267 0.267 0.267 rg
313.339 760.500 63.255 0.750 re f
313.339 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 750.645 Td /F1 9.8 Tf  [(40.6)] TJ ET
0.267 0.267 0.267 rg
375.844 760.500 68.983 0.750 re f
375.844 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 750.645 Td /F1 9.8 Tf  [(64.0)] TJ ET
0.267 0.267 0.267 rg
444.076 760.500 70.027 0.750 re f
444.076 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 750.645 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
513.353 760.500 67.522 0.750 re f
513.353 744.619 0.750 16.631 re f
580.125 744.619 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 750.645 Td /F1 9.8 Tf  [(1.3)] TJ ET
0.267 0.267 0.267 rg
26.625 744.619 106.552 0.750 re f
26.625 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 734.764 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
132.427 744.619 61.658 0.750 re f
132.427 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 734.764 Td /F1 9.8 Tf  [(27643)] TJ ET
0.267 0.267 0.267 rg
193.335 744.619 61.044 0.750 re f
193.335 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 734.764 Td /F1 9.8 Tf  [(6857)] TJ ET
0.267 0.267 0.267 rg
253.630 744.619 60.459 0.750 re f
253.630 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 734.764 Td /F1 9.8 Tf  [(17.4)] TJ ET
0.267 0.267 0.267 rg
313.339 744.619 63.255 0.750 re f
313.339 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 734.764 Td /F1 9.8 Tf  [(21.0)] TJ ET
0.267 0.267 0.267 rg
375.844 744.619 68.983 0.750 re f
375.844 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 734.764 Td /F1 9.8 Tf  [(76.9)] TJ ET
0.267 0.267 0.267 rg
444.076 744.619 70.027 0.750 re f
444.076 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 734.764 Td /F1 9.8 Tf  [(80.0)] TJ ET
0.267 0.267 0.267 rg
513.353 744.619 67.522 0.750 re f
513.353 728.737 0.750 16.631 re f
580.125 728.737 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 734.764 Td /F1 9.8 Tf  [(4.9)] TJ ET
0.267 0.267 0.267 rg
26.625 728.737 106.552 0.750 re f
26.625 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 718.883 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
132.427 728.737 61.658 0.750 re f
132.427 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 718.883 Td /F1 9.8 Tf  [(7350)] TJ ET
0.267 0.267 0.267 rg
193.335 728.737 61.044 0.750 re f
193.335 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 718.883 Td /F1 9.8 Tf  [(11856)] TJ ET
0.267 0.267 0.267 rg
253.630 728.737 60.459 0.750 re f
253.630 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 718.883 Td /F1 9.8 Tf  [(49.9)] TJ ET
0.267 0.267 0.267 rg
313.339 728.737 63.255 0.750 re f
313.339 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 718.883 Td /F1 9.8 Tf  [(34.5)] TJ ET
0.267 0.267 0.267 rg
375.844 728.737 68.983 0.750 re f
375.844 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 718.883 Td /F1 9.8 Tf  [(90.1)] TJ ET
0.267 0.267 0.267 rg
444.076 728.737 70.027 0.750 re f
444.076 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 718.883 Td /F1 9.8 Tf  [(87.4)] TJ ET
0.267 0.267 0.267 rg
513.353 728.737 67.522 0.750 re f
513.353 712.856 0.750 16.631 re f
580.125 712.856 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 718.883 Td /F1 9.8 Tf  [(12.1)] TJ ET
0.267 0.267 0.267 rg
26.625 712.856 106.552 0.750 re f
26.625 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 703.001 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
132.427 712.856 61.658 0.750 re f
132.427 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 703.001 Td /F1 9.8 Tf  [(6323)] TJ ET
0.267 0.267 0.267 rg
193.335 712.856 61.044 0.750 re f
193.335 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 703.001 Td /F1 9.8 Tf  [(8716)] TJ ET
0.267 0.267 0.267 rg
253.630 712.856 60.459 0.750 re f
253.630 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 703.001 Td /F1 9.8 Tf  [(50.4)] TJ ET
0.267 0.267 0.267 rg
313.339 712.856 63.255 0.750 re f
313.339 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 703.001 Td /F1 9.8 Tf  [(31.5)] TJ ET
0.267 0.267 0.267 rg
375.844 712.856 68.983 0.750 re f
375.844 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 703.001 Td /F1 9.8 Tf  [(83.3)] TJ ET
0.267 0.267 0.267 rg
444.076 712.856 70.027 0.750 re f
444.076 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 703.001 Td /F1 9.8 Tf  [(82.1)] TJ ET
0.267 0.267 0.267 rg
513.353 712.856 67.522 0.750 re f
513.353 696.975 0.750 16.631 re f
580.125 696.975 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 703.001 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
26.625 696.975 106.552 0.750 re f
26.625 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 687.120 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 696.975 61.658 0.750 re f
132.427 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 687.120 Td /F1 9.8 Tf  [(1028)] TJ ET
0.267 0.267 0.267 rg
193.335 696.975 61.044 0.750 re f
193.335 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 687.120 Td /F1 9.8 Tf  [(4907)] TJ ET
0.267 0.267 0.267 rg
253.630 696.975 60.459 0.750 re f
253.630 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 687.120 Td /F1 9.8 Tf  [(42.2)] TJ ET
0.267 0.267 0.267 rg
313.339 696.975 63.255 0.750 re f
313.339 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 687.120 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
375.844 696.975 68.983 0.750 re f
375.844 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 687.120 Td /F1 9.8 Tf  [(100.0)] TJ ET
0.267 0.267 0.267 rg
444.076 696.975 70.027 0.750 re f
444.076 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 687.120 Td /F1 9.8 Tf  [(82.6)] TJ ET
0.267 0.267 0.267 rg
513.353 696.975 67.522 0.750 re f
513.353 681.094 0.750 16.631 re f
580.125 681.094 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 687.120 Td /F1 9.8 Tf  [(22.0)] TJ ET
0.267 0.267 0.267 rg
26.625 681.094 106.552 0.750 re f
26.625 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 671.239 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
132.427 681.094 61.658 0.750 re f
132.427 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 671.239 Td /F1 9.8 Tf  [(901)] TJ ET
0.267 0.267 0.267 rg
193.335 681.094 61.044 0.750 re f
193.335 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 671.239 Td /F1 9.8 Tf  [(4722)] TJ ET
0.267 0.267 0.267 rg
253.630 681.094 60.459 0.750 re f
253.630 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 671.239 Td /F1 9.8 Tf  [(46.9)] TJ ET
0.267 0.267 0.267 rg
313.339 681.094 63.255 0.750 re f
313.339 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 671.239 Td /F1 9.8 Tf  [(35.9)] TJ ET
0.267 0.267 0.267 rg
375.844 681.094 68.983 0.750 re f
375.844 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 671.239 Td /F1 9.8 Tf  [(88.7)] TJ ET
0.267 0.267 0.267 rg
444.076 681.094 70.027 0.750 re f
444.076 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 671.239 Td /F1 9.8 Tf  [(78.1)] TJ ET
0.267 0.267 0.267 rg
513.353 681.094 67.522 0.750 re f
513.353 665.212 0.750 16.631 re f
580.125 665.212 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 671.239 Td /F1 9.8 Tf  [(17.2)] TJ ET
0.267 0.267 0.267 rg
26.625 665.212 106.552 0.750 re f
26.625 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 655.358 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
132.427 665.212 61.658 0.750 re f
132.427 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 655.358 Td /F1 9.8 Tf  [(278)] TJ ET
0.267 0.267 0.267 rg
193.335 665.212 61.044 0.750 re f
193.335 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 655.358 Td /F1 9.8 Tf  [(10738)] TJ ET
0.267 0.267 0.267 rg
253.630 665.212 60.459 0.750 re f
253.630 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 655.358 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
313.339 665.212 63.255 0.750 re f
313.339 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 655.358 Td /F1 9.8 Tf  [(37.7)] TJ ET
0.267 0.267 0.267 rg
375.844 665.212 68.983 0.750 re f
375.844 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 655.358 Td /F1 9.8 Tf  [(70.3)] TJ ET
0.267 0.267 0.267 rg
444.076 665.212 70.027 0.750 re f
444.076 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 655.358 Td /F1 9.8 Tf  [(83.7)] TJ ET
0.267 0.267 0.267 rg
513.353 665.212 67.522 0.750 re f
513.353 649.331 0.750 16.631 re f
580.125 649.331 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 655.358 Td /F1 9.8 Tf  [(31.9)] TJ ET
0.267 0.267 0.267 rg
26.625 649.331 106.552 0.750 re f
26.625 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 639.476 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 649.331 61.658 0.750 re f
132.427 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 639.476 Td /F1 9.8 Tf  [(263)] TJ ET
0.267 0.267 0.267 rg
193.335 649.331 61.044 0.750 re f
193.335 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 639.476 Td /F1 9.8 Tf  [(10305)] TJ ET
0.267 0.267 0.267 rg
253.630 649.331 60.459 0.750 re f
253.630 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 639.476 Td /F1 9.8 Tf  [(60.0)] TJ ET
0.267 0.267 0.267 rg
313.339 649.331 63.255 0.750 re f
313.339 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 639.476 Td /F1 9.8 Tf  [(37.7)] TJ ET
0.267 0.267 0.267 rg
375.844 649.331 68.983 0.750 re f
375.844 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 639.476 Td /F1 9.8 Tf  [(70.7)] TJ ET
0.267 0.267 0.267 rg
444.076 649.331 70.027 0.750 re f
444.076 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 639.476 Td /F1 9.8 Tf  [(83.5)] TJ ET
0.267 0.267 0.267 rg
513.353 649.331 67.522 0.750 re f
513.353 633.450 0.750 16.631 re f
580.125 633.450 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 639.476 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
26.625 633.450 106.552 0.750 re f
26.625 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 623.595 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
132.427 633.450 61.658 0.750 re f
132.427 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 623.595 Td /F1 9.8 Tf  [(144)] TJ ET
0.267 0.267 0.267 rg
193.335 633.450 61.044 0.750 re f
193.335 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 623.595 Td /F1 9.8 Tf  [(8619)] TJ ET
0.267 0.267 0.267 rg
253.630 633.450 60.459 0.750 re f
253.630 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 623.595 Td /F1 9.8 Tf  [(64.5)] TJ ET
0.267 0.267 0.267 rg
313.339 633.450 63.255 0.750 re f
313.339 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 623.595 Td /F1 9.8 Tf  [(30.3)] TJ ET
0.267 0.267 0.267 rg
375.844 633.450 68.983 0.750 re f
375.844 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 623.595 Td /F1 9.8 Tf  [(57.0)] TJ ET
0.267 0.267 0.267 rg
444.076 633.450 70.027 0.750 re f
444.076 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 623.595 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
513.353 633.450 67.522 0.750 re f
513.353 617.569 0.750 16.631 re f
580.125 617.569 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 623.595 Td /F1 9.8 Tf  [(13.5)] TJ ET
0.267 0.267 0.267 rg
26.625 617.569 106.552 0.750 re f
26.625 601.688 106.552 0.750 re f
26.625 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 607.714 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
132.427 617.569 61.658 0.750 re f
132.427 601.688 61.658 0.750 re f
132.427 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 137.677 607.714 Td /F1 9.8 Tf  [(117)] TJ ET
0.267 0.267 0.267 rg
193.335 617.569 61.044 0.750 re f
193.335 601.688 61.044 0.750 re f
193.335 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 198.585 607.714 Td /F1 9.8 Tf  [(9079)] TJ ET
0.267 0.267 0.267 rg
253.630 617.569 60.459 0.750 re f
253.630 601.688 60.459 0.750 re f
253.630 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 258.880 607.714 Td /F1 9.8 Tf  [(65.8)] TJ ET
0.267 0.267 0.267 rg
313.339 617.569 63.255 0.750 re f
313.339 601.688 63.255 0.750 re f
313.339 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 318.589 607.714 Td /F1 9.8 Tf  [(29.6)] TJ ET
0.267 0.267 0.267 rg
375.844 617.569 68.983 0.750 re f
375.844 601.688 68.983 0.750 re f
375.844 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 381.094 607.714 Td /F1 9.8 Tf  [(51.7)] TJ ET
0.267 0.267 0.267 rg
444.076 617.569 70.027 0.750 re f
444.076 601.688 70.027 0.750 re f
444.076 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 449.326 607.714 Td /F1 9.8 Tf  [(59.7)] TJ ET
0.267 0.267 0.267 rg
513.353 617.569 67.522 0.750 re f
513.353 601.688 67.522 0.750 re f
513.353 601.688 0.750 16.631 re f
580.125 601.688 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 518.603 607.714 Td /F1 9.8 Tf  [(12.6)] TJ ET
BT 26.250 537.091 Td /F4 12.0 Tf  [(Methods)] TJ ET
BT 26.250 517.137 Td /F4 9.8 Tf  [(Alignment methods)] TJ ET
BT 26.250 497.732 Td /F1 9.8 Tf  [(We estimated alignments using SAT�, Prank+GT )] TJ ET
0.267 0.267 0.267 rg
BT 241.647 497.732 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 257.910 497.732 Td /F1 9.8 Tf  [(, Muscle, Opal, MAFFT, MAFFT-PartTree )] TJ ET
0.267 0.267 0.267 rg
BT 439.942 497.732 Td /F1 9.8 Tf  [([30])] TJ ET
0.271 0.267 0.267 rg
BT 456.205 497.732 Td /F1 9.8 Tf  [(, ClustalW, and ClustalW-)] TJ ET
BT 26.250 485.827 Td /F1 9.8 Tf  [(Quicktree. The MAFFT-PartTree and ClustalW-Quicktree, methods are the variants of MAFFT and ClustalW, respectively, )] TJ ET
BT 26.250 473.922 Td /F1 9.8 Tf  [(designed for use on very large datasets. The commands used for these methods are provided in the Appendix. Due to )] TJ ET
BT 26.250 462.018 Td /F1 9.8 Tf  [(computational challenges, not all alignment methods could be run on all datasets; details of this are given in Results below.)] TJ ET
BT 26.250 442.613 Td /F1 9.8 Tf  [(The SAT� analysis we performed depended on the dataset size. The default setting for SAT� was used on the six smallest )] TJ ET
BT 26.250 430.708 Td /F1 9.8 Tf  [(datasets. The default version begins by computing four trees, formed by running RAxML to completion on MAFFT, Prank+GT )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 418.803 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 42.513 418.803 Td /F1 9.8 Tf  [(, Muscle, and ClustalW alignments. It then takes the tree/alignment pair that had the best ML score as its starting tree, and )] TJ ET
BT 26.250 406.899 Td /F1 9.8 Tf  [(iterates, alternating between alignment estimation \(using a divide-and-conquer technique that constructs alignments on subsets )] TJ ET
BT 26.250 394.994 Td /F1 9.8 Tf  [(of taxa using MAFFT, and then merges alignments using Muscle or Opal\) and tree estimation using RAxML. This iterative stage )] TJ ET
BT 26.250 383.089 Td /F1 9.8 Tf  [(lasts by default for 24 hours. The running time of SAT� thus includes a very expensive initial stage where four different two-)] TJ ET
BT 26.250 371.184 Td /F1 9.8 Tf  [(phase methods are run, and a potentially expensive second stage if the number of iterations that are run is large.)] TJ ET
BT 26.250 351.780 Td /F1 9.8 Tf  [(We modified this default setting for the four larger datasets, as follows. First, we replaced the expensive initial stage by only )] TJ ET
BT 26.250 339.875 Td /F1 9.8 Tf  [(computing RAxML on the MAFFT-PartTree alignment. Second, instead of running the next stage for 24 hours, we set the )] TJ ET
BT 26.250 327.970 Td /F1 9.8 Tf  [(number of iterations in advance. On the 16S.3 dataset we ran SAT� for five iterations, and we ran SAT� for ten iterations on the )] TJ ET
BT 26.250 316.065 Td /F1 9.8 Tf  [(16S.T dataset. We attempted to run SAT� on the largest biological dataset \(16S.B.ALL, with 27,643 sequences\), but it failed to )] TJ ET
BT 26.250 304.161 Td /F1 9.8 Tf  [(complete its first iteration. We therefore did not attempt to run SAT� on the largest dataset \(the Price 78K dataset\).)] TJ ET
BT 26.250 284.756 Td /F4 9.8 Tf  [(Maximum Likelihood Estimation Methods)] TJ ET
BT 26.250 265.351 Td /F1 9.8 Tf  [(We ran RAxML to compute trees on all but the Price 78K dataset, but tailored the specific RAxML command according to the )] TJ ET
BT 26.250 253.446 Td /F1 9.8 Tf  [(dataset size; see the Appendix for details. For the Price 78K dataset, we computed the ML tree using FastTree, since our other )] TJ ET
BT 26.250 241.542 Td /F1 9.8 Tf  [(analyses suggested that the RAxML analysis would require many months to complete.)] TJ ET
BT 26.250 222.137 Td /F4 9.8 Tf  [(Measurements)] TJ ET
BT 26.250 202.732 Td /F1 9.8 Tf  [(For each alignment produced on each dataset, we used custom code )] TJ ET
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BT 327.574 202.732 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 343.837 202.732 Td /F1 9.8 Tf  [( to compute the alignment error using the SP-FN error )] TJ ET
BT 26.250 190.827 Td /F1 9.8 Tf  [(measure, which is the proportion of the truly homologous pairs of nucleotides \(as defined by the reference alignment\) that are )] TJ ET
BT 26.250 178.923 Td /F1 9.8 Tf  [(missing in the estimated alignment )] TJ ET
0.267 0.267 0.267 rg
BT 178.516 178.923 Td /F1 9.8 Tf  [([31])] TJ ET
0.271 0.267 0.267 rg
BT 194.779 178.923 Td /F1 9.8 Tf  [(. For each tree produced on each alignment, we used custom code )] TJ ET
0.267 0.267 0.267 rg
BT 486.343 178.923 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 502.606 178.923 Td /F1 9.8 Tf  [( to compute the )] TJ ET
BT 26.250 167.018 Td /F1 9.8 Tf  [(missing branch \(or false negative\) rate, which is the proportion of the internal branches in the reference tree missing in the )] TJ ET
BT 26.250 155.113 Td /F1 9.8 Tf  [(estimated tree. We use the missing branch rate instead of the bipartition distance \(also known as the Robinson-Foulds \(RF\) )] TJ ET
BT 26.250 143.208 Td /F1 9.8 Tf  [(error rate )] TJ ET
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BT 69.053 143.208 Td /F1 9.8 Tf  [([32])] TJ ET
0.271 0.267 0.267 rg
BT 85.316 143.208 Td /F1 9.8 Tf  [(\) because the biological reference trees are not completely resolved \(high RF rates are always obtained when the )] TJ ET
BT 26.250 131.304 Td /F1 9.8 Tf  [(reference trees are highly unresolved\).)] TJ ET
BT 26.250 111.899 Td /F1 9.8 Tf  [(We also recorded the running time and the memory requirement. For the running time, we report the clock time; this is )] TJ ET
BT 26.250 99.994 Td /F1 9.8 Tf  [(approximate, since analyses were performed on machines that were not dedicated to these analyses. For the memory )] TJ ET
BT 26.250 88.089 Td /F1 9.8 Tf  [(requirement, we only report the memory available in the machine on which the method was able to run.)] TJ ET
BT 26.250 51.487 Td /F4 12.0 Tf  [(Results)] TJ ET
Q
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BT 291.710 19.825 Td /F1 11.0 Tf  [(3)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

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BT 26.250 767.476 Td /F4 9.8 Tf  [(Performance on the six smallest datasets)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(The six smallest datasets, 16S.M.aa_ag, 16S.M, 23S.M, 23S.M.aa_ag, 23S.E.aa_ag, and 23S.E, range in size from 117 taxa to )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(1028 taxa, and from 4722 sites to 10,738 sites \(see Table 1\). Thus, none of these is particularly large. On these datasets, all )] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(alignment and maximum likelihood analyses succeeded using a dedicated computing core with dedicated access to at least 512 )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(MB and at most 4 GB of main memory \(Tables 2 and 3\). The Appendix provides further details about the hardware used for )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(these computations.)] TJ ET
BT 26.250 681.048 Td /F1 9.8 Tf  [(The recorded running times for the alignment methods varied on these datasets \(Table 3\). The fastest of the alignment methods )] TJ ET
BT 26.250 669.143 Td /F1 9.8 Tf  [(is the PartTree variant of MAFFT, which completed on these datasets in at most three minutes \(most datasets completed in )] TJ ET
BT 26.250 657.238 Td /F1 9.8 Tf  [(about one minute\), and the slowest is SAT�.)] TJ ET
BT 26.250 637.833 Td /F1 9.8 Tf  [(Prank+GT tended to be the most computationally intensive of the remaining methods, using several hours on the smallest )] TJ ET
BT 26.250 625.929 Td /F1 9.8 Tf  [(datasets, on which most of the other alignment methods completed in under an hour. The next most computationally intensive )] TJ ET
BT 26.250 614.024 Td /F1 9.8 Tf  [(method was Opal. However, all alignment methods \(except for Quicktree and PartTree\) took several hours on most of these )] TJ ET
BT 26.250 602.119 Td /F1 9.8 Tf  [(�small� biological datasets. In fact, alignment estimation took more time than maximum likelihood tree estimation on many of )] TJ ET
BT 26.250 590.214 Td /F1 9.8 Tf  [(these datasets.)] TJ ET
BT 26.250 570.810 Td /F1 9.8 Tf  [(The SP-FN alignment error rates of the different alignment estimators on these smaller biological datasets also varied \(Table 2\). )] TJ ET
BT 26.250 558.905 Td /F1 9.8 Tf  [(The alignment estimation methods with the least average SP-FN error were MAFFT and SAT� with roughly 23-24% error. The )] TJ ET
BT 26.250 547.000 Td /F1 9.8 Tf  [(next group, with 27-30% error, was PartTree, Muscle, and Opal. Finally, Prank+GT, ClustalW, and QuickTree had 39-40% SP-)] TJ ET
BT 26.250 535.095 Td /F1 9.8 Tf  [(FN error.)] TJ ET
BT 26.250 515.691 Td /F1 9.8 Tf  [(Performance with respect to average missing branch rates showed SAT� and MAFFT with the lowest average missing branch )] TJ ET
BT 26.250 503.786 Td /F1 9.8 Tf  [(rates of 6-8%, followed by PartTree, Prank+GT, Muscle, and ClustalW with average missing branch rates of 13-16%, and then )] TJ ET
BT 26.250 491.881 Td /F1 9.8 Tf  [(by Opal and Quicktree with 18-19% average missing branch rates. Thus, alignment error, measured using SP-FN, is not )] TJ ET
BT 26.250 479.976 Td /F1 9.8 Tf  [(particularly predictive of tree error; for example, Opal and Prank+GT change their positions quite dramatically with respect to )] TJ ET
BT 26.250 468.072 Td /F1 9.8 Tf  [(these criteria.)] TJ ET
BT 26.250 448.667 Td /F4 9.8 Tf  [(Performance on the four largest datasets)] TJ ET
BT 26.250 429.262 Td /F1 9.8 Tf  [(The four largest datasets consist of three biological datasets ranging in size from 6323 to 27,643 taxa, and having from 6,857 to )] TJ ET
BT 26.250 417.357 Td /F1 9.8 Tf  [(11,856 sites; in addition, we have one simulated dataset with 78,132 taxa and 1287 sites. Thus, these four datasets present )] TJ ET
BT 26.250 405.453 Td /F1 9.8 Tf  [(substantial computational challenges. Table 4 gives the comparison between methods in terms of alignment and tree accuracy, )] TJ ET
BT 26.250 393.548 Td /F1 9.8 Tf  [(and Table 5 gives the running time of these methods on the large datasets.)] TJ ET
BT 26.250 374.143 Td /F1 9.8 Tf  [(We focus first on the three biological datasets, which range in size from 6323 sequences to 27,643 sequences. Many methods )] TJ ET
BT 26.250 362.238 Td /F1 9.8 Tf  [(aborted on these datasets: five failures on the 16S.B.ALL dataset \(the largest\), and three on the 16S.3 dataset. Only two )] TJ ET
BT 26.250 350.334 Td /F1 9.8 Tf  [(alignment methods completed successfully on the 16S.B.ALL dataset, six on the 16S.T dataset, and four on the 16S.3 dataset. )] TJ ET
BT 26.250 338.429 Td /F1 9.8 Tf  [(In addition, several methods ran for 35 days on a machine with 256 GB of main memory without returning an alignment, and are )] TJ ET
BT 26.250 326.524 Td /F1 9.8 Tf  [(still running \(�s.r.�\): Muscle is still running on all three of the largest biological datasets and Prank+GT is still running on the )] TJ ET
BT 26.250 314.619 Td /F1 9.8 Tf  [(16S.T dataset. Thus, these datasets are very difficult for these alignment methods.)] TJ ET
BT 26.250 295.215 Td /F1 9.8 Tf  [(The smallest of these datasets is 16S.3, with 6323 sequences. Only four methods completed on the 16S.3 dataset, three )] TJ ET
BT 26.250 283.310 Td /F1 9.8 Tf  [(failures occurred \(MAFFT, Prank+GT, and Opal\), and one method \(Muscle\) is still running. In terms of alignment error, PartTree )] TJ ET
BT 26.250 271.405 Td /F1 9.8 Tf  [(had less error than CLustalW and Quicktree. In terms of tree error, SAT� had the least error \(7%\), followed by ML\(ClustalW\) )] TJ ET
BT 26.250 259.500 Td /F1 9.8 Tf  [(with 9.29%, and then ML\(PartTree\) with 11.83%. ML\(Quicktree\) had very high error of 31.47%.)] TJ ET
BT 26.250 240.096 Td /F1 9.8 Tf  [(On the next largest CRW dataset, 16S.T \(with 7350 sequences\), six methods completed, two methods \(Prank+GT and Muscle\) )] TJ ET
BT 26.250 228.191 Td /F1 9.8 Tf  [(are still running, and no failures occurred. In terms of alignment SP-FN error, MAFFT is best, followed by PartTree, then SAT�, )] TJ ET
BT 26.250 216.286 Td /F1 9.8 Tf  [(and then Opal, but all four methods are fairly close in SP-FN error \(roughly 31%-39%\). ClustalW and Quicktree have much )] TJ ET
BT 26.250 204.381 Td /F1 9.8 Tf  [(higher SP-FN error rates \(56% and 63%\). In terms of tree error, ML\(MAFFT\) is best \(7.29%\) followed closely by SAT� \(7.59%\), )] TJ ET
BT 26.250 192.477 Td /F1 9.8 Tf  [(and then by ML\(ClustalW\) at 10.21% error. ML\(PartTree\) and ML\(Opal\) are next, at 16.73% and 18.62%, respectively. Finally, )] TJ ET
BT 26.250 180.572 Td /F1 9.8 Tf  [(ML\(Quicktree\) has the highest error at 34.23%.)] TJ ET
BT 26.250 161.167 Td /F1 9.8 Tf  [(The largest of these three CRW datasets is the 16S.B.ALL dataset, which contains 27,643 sequences. Only two methods, )] TJ ET
BT 26.250 149.262 Td /F1 9.8 Tf  [(PartTree and QuickTree, succeeded in producing alignments on the 16S.B.ALL dataset. \(Muscle is still running; all other )] TJ ET
BT 26.250 137.358 Td /F1 9.8 Tf  [(methods have aborted on this dataset.\) PartTree�s alignment has 41.7% error and QuickTree�s alignment has 54.4% error. )] TJ ET
BT 26.250 125.453 Td /F1 9.8 Tf  [(Maximum likelihood analyses of these two alignments produced trees with high error: 13% for ML\(QuickTree\) and 32% for )] TJ ET
BT 26.250 113.548 Td /F1 9.8 Tf  [(ML\(PartTree\). Running times for Quicktree and PartTree alignment methods were very large�175 and 262 hours, respectively. )] TJ ET
BT 26.250 101.643 Td /F1 9.8 Tf  [(The maximum likelihood analyses of these alignments took even longer, 1328 and 1254 hours, respectively. The memory )] TJ ET
BT 26.250 89.739 Td /F1 9.8 Tf  [(requirements for these methods are unknown, but each failed during an individual run with dedicated access to all 32 GB of )] TJ ET
BT 26.250 77.834 Td /F1 9.8 Tf  [(main memory on one machine and succeeded with dedicated access to all 256 GB of main memory on another machine.)] TJ ET
BT 26.250 58.429 Td /F1 9.8 Tf  [(A comparison of the alignment methods on the 16S.3 and 16S.T datasets shows that PartTree is extremely fast on these )] TJ ET
BT 26.250 46.524 Td /F1 9.8 Tf  [(datasets, finishing in 1.3 hours on the 16S.T dataset and in less than an hour on the 16S.3 dataset, and QuickTree is in second )] TJ ET
Q
q
15.000 32.239 577.500 744.761 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F4 9.8 Tf  [(Performance on the six smallest datasets)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(The six smallest datasets, 16S.M.aa_ag, 16S.M, 23S.M, 23S.M.aa_ag, 23S.E.aa_ag, and 23S.E, range in size from 117 taxa to )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(1028 taxa, and from 4722 sites to 10,738 sites \(see Table 1\). Thus, none of these is particularly large. On these datasets, all )] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(alignment and maximum likelihood analyses succeeded using a dedicated computing core with dedicated access to at least 512 )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(MB and at most 4 GB of main memory \(Tables 2 and 3\). The Appendix provides further details about the hardware used for )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(these computations.)] TJ ET
BT 26.250 681.048 Td /F1 9.8 Tf  [(The recorded running times for the alignment methods varied on these datasets \(Table 3\). The fastest of the alignment methods )] TJ ET
BT 26.250 669.143 Td /F1 9.8 Tf  [(is the PartTree variant of MAFFT, which completed on these datasets in at most three minutes \(most datasets completed in )] TJ ET
BT 26.250 657.238 Td /F1 9.8 Tf  [(about one minute\), and the slowest is SAT�.)] TJ ET
BT 26.250 637.833 Td /F1 9.8 Tf  [(Prank+GT tended to be the most computationally intensive of the remaining methods, using several hours on the smallest )] TJ ET
BT 26.250 625.929 Td /F1 9.8 Tf  [(datasets, on which most of the other alignment methods completed in under an hour. The next most computationally intensive )] TJ ET
BT 26.250 614.024 Td /F1 9.8 Tf  [(method was Opal. However, all alignment methods \(except for Quicktree and PartTree\) took several hours on most of these )] TJ ET
BT 26.250 602.119 Td /F1 9.8 Tf  [(�small� biological datasets. In fact, alignment estimation took more time than maximum likelihood tree estimation on many of )] TJ ET
BT 26.250 590.214 Td /F1 9.8 Tf  [(these datasets.)] TJ ET
BT 26.250 570.810 Td /F1 9.8 Tf  [(The SP-FN alignment error rates of the different alignment estimators on these smaller biological datasets also varied \(Table 2\). )] TJ ET
BT 26.250 558.905 Td /F1 9.8 Tf  [(The alignment estimation methods with the least average SP-FN error were MAFFT and SAT� with roughly 23-24% error. The )] TJ ET
BT 26.250 547.000 Td /F1 9.8 Tf  [(next group, with 27-30% error, was PartTree, Muscle, and Opal. Finally, Prank+GT, ClustalW, and QuickTree had 39-40% SP-)] TJ ET
BT 26.250 535.095 Td /F1 9.8 Tf  [(FN error.)] TJ ET
BT 26.250 515.691 Td /F1 9.8 Tf  [(Performance with respect to average missing branch rates showed SAT� and MAFFT with the lowest average missing branch )] TJ ET
BT 26.250 503.786 Td /F1 9.8 Tf  [(rates of 6-8%, followed by PartTree, Prank+GT, Muscle, and ClustalW with average missing branch rates of 13-16%, and then )] TJ ET
BT 26.250 491.881 Td /F1 9.8 Tf  [(by Opal and Quicktree with 18-19% average missing branch rates. Thus, alignment error, measured using SP-FN, is not )] TJ ET
BT 26.250 479.976 Td /F1 9.8 Tf  [(particularly predictive of tree error; for example, Opal and Prank+GT change their positions quite dramatically with respect to )] TJ ET
BT 26.250 468.072 Td /F1 9.8 Tf  [(these criteria.)] TJ ET
BT 26.250 448.667 Td /F4 9.8 Tf  [(Performance on the four largest datasets)] TJ ET
BT 26.250 429.262 Td /F1 9.8 Tf  [(The four largest datasets consist of three biological datasets ranging in size from 6323 to 27,643 taxa, and having from 6,857 to )] TJ ET
BT 26.250 417.357 Td /F1 9.8 Tf  [(11,856 sites; in addition, we have one simulated dataset with 78,132 taxa and 1287 sites. Thus, these four datasets present )] TJ ET
BT 26.250 405.453 Td /F1 9.8 Tf  [(substantial computational challenges. Table 4 gives the comparison between methods in terms of alignment and tree accuracy, )] TJ ET
BT 26.250 393.548 Td /F1 9.8 Tf  [(and Table 5 gives the running time of these methods on the large datasets.)] TJ ET
BT 26.250 374.143 Td /F1 9.8 Tf  [(We focus first on the three biological datasets, which range in size from 6323 sequences to 27,643 sequences. Many methods )] TJ ET
BT 26.250 362.238 Td /F1 9.8 Tf  [(aborted on these datasets: five failures on the 16S.B.ALL dataset \(the largest\), and three on the 16S.3 dataset. Only two )] TJ ET
BT 26.250 350.334 Td /F1 9.8 Tf  [(alignment methods completed successfully on the 16S.B.ALL dataset, six on the 16S.T dataset, and four on the 16S.3 dataset. )] TJ ET
BT 26.250 338.429 Td /F1 9.8 Tf  [(In addition, several methods ran for 35 days on a machine with 256 GB of main memory without returning an alignment, and are )] TJ ET
BT 26.250 326.524 Td /F1 9.8 Tf  [(still running \(�s.r.�\): Muscle is still running on all three of the largest biological datasets and Prank+GT is still running on the )] TJ ET
BT 26.250 314.619 Td /F1 9.8 Tf  [(16S.T dataset. Thus, these datasets are very difficult for these alignment methods.)] TJ ET
BT 26.250 295.215 Td /F1 9.8 Tf  [(The smallest of these datasets is 16S.3, with 6323 sequences. Only four methods completed on the 16S.3 dataset, three )] TJ ET
BT 26.250 283.310 Td /F1 9.8 Tf  [(failures occurred \(MAFFT, Prank+GT, and Opal\), and one method \(Muscle\) is still running. In terms of alignment error, PartTree )] TJ ET
BT 26.250 271.405 Td /F1 9.8 Tf  [(had less error than CLustalW and Quicktree. In terms of tree error, SAT� had the least error \(7%\), followed by ML\(ClustalW\) )] TJ ET
BT 26.250 259.500 Td /F1 9.8 Tf  [(with 9.29%, and then ML\(PartTree\) with 11.83%. ML\(Quicktree\) had very high error of 31.47%.)] TJ ET
BT 26.250 240.096 Td /F1 9.8 Tf  [(On the next largest CRW dataset, 16S.T \(with 7350 sequences\), six methods completed, two methods \(Prank+GT and Muscle\) )] TJ ET
BT 26.250 228.191 Td /F1 9.8 Tf  [(are still running, and no failures occurred. In terms of alignment SP-FN error, MAFFT is best, followed by PartTree, then SAT�, )] TJ ET
BT 26.250 216.286 Td /F1 9.8 Tf  [(and then Opal, but all four methods are fairly close in SP-FN error \(roughly 31%-39%\). ClustalW and Quicktree have much )] TJ ET
BT 26.250 204.381 Td /F1 9.8 Tf  [(higher SP-FN error rates \(56% and 63%\). In terms of tree error, ML\(MAFFT\) is best \(7.29%\) followed closely by SAT� \(7.59%\), )] TJ ET
BT 26.250 192.477 Td /F1 9.8 Tf  [(and then by ML\(ClustalW\) at 10.21% error. ML\(PartTree\) and ML\(Opal\) are next, at 16.73% and 18.62%, respectively. Finally, )] TJ ET
BT 26.250 180.572 Td /F1 9.8 Tf  [(ML\(Quicktree\) has the highest error at 34.23%.)] TJ ET
BT 26.250 161.167 Td /F1 9.8 Tf  [(The largest of these three CRW datasets is the 16S.B.ALL dataset, which contains 27,643 sequences. Only two methods, )] TJ ET
BT 26.250 149.262 Td /F1 9.8 Tf  [(PartTree and QuickTree, succeeded in producing alignments on the 16S.B.ALL dataset. \(Muscle is still running; all other )] TJ ET
BT 26.250 137.358 Td /F1 9.8 Tf  [(methods have aborted on this dataset.\) PartTree�s alignment has 41.7% error and QuickTree�s alignment has 54.4% error. )] TJ ET
BT 26.250 125.453 Td /F1 9.8 Tf  [(Maximum likelihood analyses of these two alignments produced trees with high error: 13% for ML\(QuickTree\) and 32% for )] TJ ET
BT 26.250 113.548 Td /F1 9.8 Tf  [(ML\(PartTree\). Running times for Quicktree and PartTree alignment methods were very large�175 and 262 hours, respectively. )] TJ ET
BT 26.250 101.643 Td /F1 9.8 Tf  [(The maximum likelihood analyses of these alignments took even longer, 1328 and 1254 hours, respectively. The memory )] TJ ET
BT 26.250 89.739 Td /F1 9.8 Tf  [(requirements for these methods are unknown, but each failed during an individual run with dedicated access to all 32 GB of )] TJ ET
BT 26.250 77.834 Td /F1 9.8 Tf  [(main memory on one machine and succeeded with dedicated access to all 256 GB of main memory on another machine.)] TJ ET
BT 26.250 58.429 Td /F1 9.8 Tf  [(A comparison of the alignment methods on the 16S.3 and 16S.T datasets shows that PartTree is extremely fast on these )] TJ ET
BT 26.250 46.524 Td /F1 9.8 Tf  [(datasets, finishing in 1.3 hours on the 16S.T dataset and in less than an hour on the 16S.3 dataset, and QuickTree is in second )] TJ ET
Q
q
15.000 32.239 577.500 744.761 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F4 9.8 Tf  [(Performance on the six smallest datasets)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(The six smallest datasets, 16S.M.aa_ag, 16S.M, 23S.M, 23S.M.aa_ag, 23S.E.aa_ag, and 23S.E, range in size from 117 taxa to )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(1028 taxa, and from 4722 sites to 10,738 sites \(see Table 1\). Thus, none of these is particularly large. On these datasets, all )] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(alignment and maximum likelihood analyses succeeded using a dedicated computing core with dedicated access to at least 512 )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(MB and at most 4 GB of main memory \(Tables 2 and 3\). The Appendix provides further details about the hardware used for )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(these computations.)] TJ ET
BT 26.250 681.048 Td /F1 9.8 Tf  [(The recorded running times for the alignment methods varied on these datasets \(Table 3\). The fastest of the alignment methods )] TJ ET
BT 26.250 669.143 Td /F1 9.8 Tf  [(is the PartTree variant of MAFFT, which completed on these datasets in at most three minutes \(most datasets completed in )] TJ ET
BT 26.250 657.238 Td /F1 9.8 Tf  [(about one minute\), and the slowest is SAT�.)] TJ ET
BT 26.250 637.833 Td /F1 9.8 Tf  [(Prank+GT tended to be the most computationally intensive of the remaining methods, using several hours on the smallest )] TJ ET
BT 26.250 625.929 Td /F1 9.8 Tf  [(datasets, on which most of the other alignment methods completed in under an hour. The next most computationally intensive )] TJ ET
BT 26.250 614.024 Td /F1 9.8 Tf  [(method was Opal. However, all alignment methods \(except for Quicktree and PartTree\) took several hours on most of these )] TJ ET
BT 26.250 602.119 Td /F1 9.8 Tf  [(�small� biological datasets. In fact, alignment estimation took more time than maximum likelihood tree estimation on many of )] TJ ET
BT 26.250 590.214 Td /F1 9.8 Tf  [(these datasets.)] TJ ET
BT 26.250 570.810 Td /F1 9.8 Tf  [(The SP-FN alignment error rates of the different alignment estimators on these smaller biological datasets also varied \(Table 2\). )] TJ ET
BT 26.250 558.905 Td /F1 9.8 Tf  [(The alignment estimation methods with the least average SP-FN error were MAFFT and SAT� with roughly 23-24% error. The )] TJ ET
BT 26.250 547.000 Td /F1 9.8 Tf  [(next group, with 27-30% error, was PartTree, Muscle, and Opal. Finally, Prank+GT, ClustalW, and QuickTree had 39-40% SP-)] TJ ET
BT 26.250 535.095 Td /F1 9.8 Tf  [(FN error.)] TJ ET
BT 26.250 515.691 Td /F1 9.8 Tf  [(Performance with respect to average missing branch rates showed SAT� and MAFFT with the lowest average missing branch )] TJ ET
BT 26.250 503.786 Td /F1 9.8 Tf  [(rates of 6-8%, followed by PartTree, Prank+GT, Muscle, and ClustalW with average missing branch rates of 13-16%, and then )] TJ ET
BT 26.250 491.881 Td /F1 9.8 Tf  [(by Opal and Quicktree with 18-19% average missing branch rates. Thus, alignment error, measured using SP-FN, is not )] TJ ET
BT 26.250 479.976 Td /F1 9.8 Tf  [(particularly predictive of tree error; for example, Opal and Prank+GT change their positions quite dramatically with respect to )] TJ ET
BT 26.250 468.072 Td /F1 9.8 Tf  [(these criteria.)] TJ ET
BT 26.250 448.667 Td /F4 9.8 Tf  [(Performance on the four largest datasets)] TJ ET
BT 26.250 429.262 Td /F1 9.8 Tf  [(The four largest datasets consist of three biological datasets ranging in size from 6323 to 27,643 taxa, and having from 6,857 to )] TJ ET
BT 26.250 417.357 Td /F1 9.8 Tf  [(11,856 sites; in addition, we have one simulated dataset with 78,132 taxa and 1287 sites. Thus, these four datasets present )] TJ ET
BT 26.250 405.453 Td /F1 9.8 Tf  [(substantial computational challenges. Table 4 gives the comparison between methods in terms of alignment and tree accuracy, )] TJ ET
BT 26.250 393.548 Td /F1 9.8 Tf  [(and Table 5 gives the running time of these methods on the large datasets.)] TJ ET
BT 26.250 374.143 Td /F1 9.8 Tf  [(We focus first on the three biological datasets, which range in size from 6323 sequences to 27,643 sequences. Many methods )] TJ ET
BT 26.250 362.238 Td /F1 9.8 Tf  [(aborted on these datasets: five failures on the 16S.B.ALL dataset \(the largest\), and three on the 16S.3 dataset. Only two )] TJ ET
BT 26.250 350.334 Td /F1 9.8 Tf  [(alignment methods completed successfully on the 16S.B.ALL dataset, six on the 16S.T dataset, and four on the 16S.3 dataset. )] TJ ET
BT 26.250 338.429 Td /F1 9.8 Tf  [(In addition, several methods ran for 35 days on a machine with 256 GB of main memory without returning an alignment, and are )] TJ ET
BT 26.250 326.524 Td /F1 9.8 Tf  [(still running \(�s.r.�\): Muscle is still running on all three of the largest biological datasets and Prank+GT is still running on the )] TJ ET
BT 26.250 314.619 Td /F1 9.8 Tf  [(16S.T dataset. Thus, these datasets are very difficult for these alignment methods.)] TJ ET
BT 26.250 295.215 Td /F1 9.8 Tf  [(The smallest of these datasets is 16S.3, with 6323 sequences. Only four methods completed on the 16S.3 dataset, three )] TJ ET
BT 26.250 283.310 Td /F1 9.8 Tf  [(failures occurred \(MAFFT, Prank+GT, and Opal\), and one method \(Muscle\) is still running. In terms of alignment error, PartTree )] TJ ET
BT 26.250 271.405 Td /F1 9.8 Tf  [(had less error than CLustalW and Quicktree. In terms of tree error, SAT� had the least error \(7%\), followed by ML\(ClustalW\) )] TJ ET
BT 26.250 259.500 Td /F1 9.8 Tf  [(with 9.29%, and then ML\(PartTree\) with 11.83%. ML\(Quicktree\) had very high error of 31.47%.)] TJ ET
BT 26.250 240.096 Td /F1 9.8 Tf  [(On the next largest CRW dataset, 16S.T \(with 7350 sequences\), six methods completed, two methods \(Prank+GT and Muscle\) )] TJ ET
BT 26.250 228.191 Td /F1 9.8 Tf  [(are still running, and no failures occurred. In terms of alignment SP-FN error, MAFFT is best, followed by PartTree, then SAT�, )] TJ ET
BT 26.250 216.286 Td /F1 9.8 Tf  [(and then Opal, but all four methods are fairly close in SP-FN error \(roughly 31%-39%\). ClustalW and Quicktree have much )] TJ ET
BT 26.250 204.381 Td /F1 9.8 Tf  [(higher SP-FN error rates \(56% and 63%\). In terms of tree error, ML\(MAFFT\) is best \(7.29%\) followed closely by SAT� \(7.59%\), )] TJ ET
BT 26.250 192.477 Td /F1 9.8 Tf  [(and then by ML\(ClustalW\) at 10.21% error. ML\(PartTree\) and ML\(Opal\) are next, at 16.73% and 18.62%, respectively. Finally, )] TJ ET
BT 26.250 180.572 Td /F1 9.8 Tf  [(ML\(Quicktree\) has the highest error at 34.23%.)] TJ ET
BT 26.250 161.167 Td /F1 9.8 Tf  [(The largest of these three CRW datasets is the 16S.B.ALL dataset, which contains 27,643 sequences. Only two methods, )] TJ ET
BT 26.250 149.262 Td /F1 9.8 Tf  [(PartTree and QuickTree, succeeded in producing alignments on the 16S.B.ALL dataset. \(Muscle is still running; all other )] TJ ET
BT 26.250 137.358 Td /F1 9.8 Tf  [(methods have aborted on this dataset.\) PartTree�s alignment has 41.7% error and QuickTree�s alignment has 54.4% error. )] TJ ET
BT 26.250 125.453 Td /F1 9.8 Tf  [(Maximum likelihood analyses of these two alignments produced trees with high error: 13% for ML\(QuickTree\) and 32% for )] TJ ET
BT 26.250 113.548 Td /F1 9.8 Tf  [(ML\(PartTree\). Running times for Quicktree and PartTree alignment methods were very large�175 and 262 hours, respectively. )] TJ ET
BT 26.250 101.643 Td /F1 9.8 Tf  [(The maximum likelihood analyses of these alignments took even longer, 1328 and 1254 hours, respectively. The memory )] TJ ET
BT 26.250 89.739 Td /F1 9.8 Tf  [(requirements for these methods are unknown, but each failed during an individual run with dedicated access to all 32 GB of )] TJ ET
BT 26.250 77.834 Td /F1 9.8 Tf  [(main memory on one machine and succeeded with dedicated access to all 256 GB of main memory on another machine.)] TJ ET
BT 26.250 58.429 Td /F1 9.8 Tf  [(A comparison of the alignment methods on the 16S.3 and 16S.T datasets shows that PartTree is extremely fast on these )] TJ ET
BT 26.250 46.524 Td /F1 9.8 Tf  [(datasets, finishing in 1.3 hours on the 16S.T dataset and in less than an hour on the 16S.3 dataset, and QuickTree is in second )] TJ ET
Q
q
0.000 0.000 0.000 rg
BT 291.710 19.825 Td /F1 11.0 Tf  [(4)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

Q
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0.271 0.267 0.267 rg
q
15.000 29.743 577.500 747.257 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(place at 41.2 and 20.4 hours, respectively. ClustalW and SAT� take much longer: ClustalW uses 506 hours on the 16S.T )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(dataset and 440 hours on the 16S.3 dataset, while SAT� takes 1505.8 hours on the 16S.T dataset and 563.2 hours on the )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(16S.3 dataset. \(The difference in running time for SAT� on these two datasets is because SAT� runs for ten iterations on the )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(16S.T dataset, but only five iterations on the 16S.3 dataset.\) Maximum likelihood analyses of the four alignment methods that )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(completed on these two datasets were also computationally intensive: on the 16S.T dataset, RAxML analyses ranged from 121 )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(to 156 hours \(depending on the alignment\), while on the 16S.3 dataset, these analyses ranged from 55 to 91 hours. We were )] TJ ET
BT 26.250 696.048 Td /F1 9.8 Tf  [(able to run SAT� successfuly on the 16S.T and 16S.3 datasets using machines with 32 GB main memory available for each )] TJ ET
BT 26.250 684.143 Td /F1 9.8 Tf  [(run, whereas MAFFT and Opal both were unable to analyze the 16S.T dataset on a machine with 32 GB main memory )] TJ ET
BT 26.250 672.238 Td /F1 9.8 Tf  [(available for each run and failed on the 16S.3 dataset.)] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(The Price 78K dataset is the largest of these datasets, and so presents a particularly difficult challenge to the alignment )] TJ ET
BT 26.250 640.929 Td /F1 9.8 Tf  [(methods. On the other hand, the model condition under which this dataset was generated produced a very low number of indels )] TJ ET
BT 26.250 629.024 Td /F1 9.8 Tf  [(\(0.6% of the true matrix is occupied by gaps, two orders of magnitude smaller than what we see for the biological datasets\). )] TJ ET
BT 26.250 617.119 Td /F1 9.8 Tf  [(Therefore, the Price 78K dataset represents primarily a scalability test � i.e., can the alignment method be run on this dataset? � )] TJ ET
BT 26.250 605.214 Td /F1 9.8 Tf  [(rather than a test of accuracy for the resultant alignment. Because of the failures of most alignment methods on the 16S.B.ALL )] TJ ET
BT 26.250 593.310 Td /F1 9.8 Tf  [(dataset, we only attempted to run the Quicktree and PartTree alignments on the Price 78K dataset. Quicktree failed on this )] TJ ET
BT 26.250 581.405 Td /F1 9.8 Tf  [(dataset, but PartTree completed. PartTree used 71.5 hours to complete on this dataset \(less than it used on the 16S.B.ALL )] TJ ET
BT 26.250 569.500 Td /F1 9.8 Tf  [(dataset\). We used FastTree to compute an ML tree on the PartTree alignment, which produced a tree with 9.14% missing )] TJ ET
BT 26.250 557.595 Td /F1 9.8 Tf  [(branch rate in 2.9 hours. While this is a fairly high error rate, by comparison, FastTree on the true alignment \(which took 3.7 )] TJ ET
BT 26.250 545.691 Td /F1 9.8 Tf  [(hours to complete\) had 8% missing branch rate. Since the true alignment has a relatively low number of sites \(1287\) for the )] TJ ET
BT 26.250 533.786 Td /F1 9.8 Tf  [(large number of leaves \(78,132\), it seems likely that the 8% of the edges missing in the FastTree analysis of the true alignment )] TJ ET
BT 26.250 521.881 Td /F1 9.8 Tf  [(are weakly supported. Therefore, the FastTree analysis of the PartTree alignment of the Price 78K dataset is actually highly )] TJ ET
BT 26.250 509.976 Td /F1 9.8 Tf  [(accurate.)] TJ ET
BT 26.250 490.572 Td /F4 9.8 Tf  [(Table 2: Comparison of missing branch rates and alignment SP-FN errors on the six smallest datasets. )] TJ ET
BT 504.683 490.572 Td /F1 9.8 Tf  [( Each row gives )] TJ ET
BT 26.250 478.667 Td /F1 9.8 Tf  [(results for a method, and each column corresponds to a dataset. All analyses succeeded using a dedicated computing core with )] TJ ET
BT 26.250 466.762 Td /F1 9.8 Tf  [(dedicated access to at least 512 MB and at most 4 GB of main memory. The Appendix provides further details about the )] TJ ET
BT 26.250 454.857 Td /F1 9.8 Tf  [(hardware used for these computations. Missing branch rates \(%\) are with respect to the reference tree. Alignment SP-FN errors )] TJ ET
BT 26.250 442.953 Td /F1 9.8 Tf  [(\(%\) are with respect to the curated alignment. ML tree estimation was performed using RAxML.)] TJ ET
1.000 1.000 1.000 rg
26.250 91.053 555.000 342.019 re f
0.267 0.267 0.267 rg
26.625 431.947 107.042 0.750 re f
26.625 416.065 0.750 16.631 re f
132.917 431.947 86.616 0.750 re f
219.533 431.947 48.284 0.750 re f
267.817 431.947 48.284 0.750 re f
316.101 431.947 86.241 0.750 re f
402.342 431.947 84.180 0.750 re f
486.522 431.947 46.599 0.750 re f
132.917 416.065 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 422.092 Td /F4 9.8 Tf  [(Missing branch rate \(%\))] TJ ET
0.267 0.267 0.267 rg
532.371 431.947 48.504 0.750 re f
532.371 416.065 0.750 16.631 re f
580.125 416.065 0.750 16.631 re f
26.625 416.065 107.042 0.750 re f
26.625 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 406.210 Td /F1 9.8 Tf  [(Method)] TJ ET
0.267 0.267 0.267 rg
132.917 416.065 86.991 0.750 re f
132.917 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 406.210 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
219.158 416.065 49.034 0.750 re f
219.158 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 406.210 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
267.442 416.065 49.034 0.750 re f
267.442 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 406.210 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
315.726 416.065 86.991 0.750 re f
315.726 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 406.210 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
401.967 416.065 84.930 0.750 re f
401.967 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 406.210 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
486.147 416.065 46.974 0.750 re f
486.147 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 406.210 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
532.371 416.065 48.504 0.750 re f
532.371 392.553 0.750 24.263 re f
580.125 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 406.210 Td /F1 9.8 Tf  [(Avg )] TJ ET
BT 537.621 398.579 Td /F1 9.8 Tf  [(error)] TJ ET
0.267 0.267 0.267 rg
26.625 392.553 107.042 0.750 re f
26.625 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 382.698 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
132.917 392.553 86.991 0.750 re f
132.917 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 382.698 Td /F1 9.8 Tf  [(5.08)] TJ ET
0.267 0.267 0.267 rg
219.158 392.553 49.034 0.750 re f
219.158 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 382.698 Td /F1 9.8 Tf  [(5.70)] TJ ET
0.267 0.267 0.267 rg
267.442 392.553 49.034 0.750 re f
267.442 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 382.698 Td /F1 9.8 Tf  [(10.12)] TJ ET
0.267 0.267 0.267 rg
315.726 392.553 86.991 0.750 re f
315.726 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 382.698 Td /F1 9.8 Tf  [(10.90)] TJ ET
0.267 0.267 0.267 rg
401.967 392.553 84.930 0.750 re f
401.967 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 382.698 Td /F1 9.8 Tf  [(6.59)] TJ ET
0.267 0.267 0.267 rg
486.147 392.553 46.974 0.750 re f
486.147 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 382.698 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 392.553 48.504 0.750 re f
532.371 376.672 0.750 16.631 re f
580.125 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 382.698 Td /F1 9.8 Tf  [(7.51)] TJ ET
0.267 0.267 0.267 rg
26.625 376.672 107.042 0.750 re f
26.625 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 366.817 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
132.917 376.672 86.991 0.750 re f
132.917 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 366.817 Td /F1 9.8 Tf  [(4.16)] TJ ET
0.267 0.267 0.267 rg
219.158 376.672 49.034 0.750 re f
219.158 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 366.817 Td /F1 9.8 Tf  [(5.70)] TJ ET
0.267 0.267 0.267 rg
267.442 376.672 49.034 0.750 re f
267.442 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 366.817 Td /F1 9.8 Tf  [(11.90)] TJ ET
0.267 0.267 0.267 rg
315.726 376.672 86.991 0.750 re f
315.726 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 366.817 Td /F1 9.8 Tf  [(10.90)] TJ ET
0.267 0.267 0.267 rg
401.967 376.672 84.930 0.750 re f
401.967 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 366.817 Td /F1 9.8 Tf  [(7.69)] TJ ET
0.267 0.267 0.267 rg
486.147 376.672 46.974 0.750 re f
486.147 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 366.817 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 376.672 48.504 0.750 re f
532.371 360.790 0.750 16.631 re f
580.125 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 366.817 Td /F1 9.8 Tf  [(7.84)] TJ ET
0.267 0.267 0.267 rg
26.625 360.790 107.042 0.750 re f
26.625 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 350.935 Td /F1 9.8 Tf  [(ML\(MAFFT-PartTree\))] TJ ET
0.267 0.267 0.267 rg
132.917 360.790 86.991 0.750 re f
132.917 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 350.935 Td /F1 9.8 Tf  [(10.62)] TJ ET
0.267 0.267 0.267 rg
219.158 360.790 49.034 0.750 re f
219.158 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 350.935 Td /F1 9.8 Tf  [(8.79)] TJ ET
0.267 0.267 0.267 rg
267.442 360.790 49.034 0.750 re f
267.442 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 350.935 Td /F1 9.8 Tf  [(22.02)] TJ ET
0.267 0.267 0.267 rg
315.726 360.790 86.991 0.750 re f
315.726 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 350.935 Td /F1 9.8 Tf  [(20.51)] TJ ET
0.267 0.267 0.267 rg
401.967 360.790 84.930 0.750 re f
401.967 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 350.935 Td /F1 9.8 Tf  [(14.29)] TJ ET
0.267 0.267 0.267 rg
486.147 360.790 46.974 0.750 re f
486.147 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 350.935 Td /F1 9.8 Tf  [(5.33)] TJ ET
0.267 0.267 0.267 rg
532.371 360.790 48.504 0.750 re f
532.371 344.909 0.750 16.631 re f
580.125 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 350.935 Td /F1 9.8 Tf  [(13.59)] TJ ET
0.267 0.267 0.267 rg
26.625 344.909 107.042 0.750 re f
26.625 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 335.054 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
132.917 344.909 86.991 0.750 re f
132.917 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 335.054 Td /F1 9.8 Tf  [(7.62)] TJ ET
0.267 0.267 0.267 rg
219.158 344.909 49.034 0.750 re f
219.158 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 335.054 Td /F1 9.8 Tf  [(11.40)] TJ ET
0.267 0.267 0.267 rg
267.442 344.909 49.034 0.750 re f
267.442 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 335.054 Td /F1 9.8 Tf  [(14.29)] TJ ET
0.267 0.267 0.267 rg
315.726 344.909 86.991 0.750 re f
315.726 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 335.054 Td /F1 9.8 Tf  [(19.23)] TJ ET
0.267 0.267 0.267 rg
401.967 344.909 84.930 0.750 re f
401.967 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 335.054 Td /F1 9.8 Tf  [(27.47)] TJ ET
0.267 0.267 0.267 rg
486.147 344.909 46.974 0.750 re f
486.147 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 335.054 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 344.909 48.504 0.750 re f
532.371 329.028 0.750 16.631 re f
580.125 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 335.054 Td /F1 9.8 Tf  [(14.45)] TJ ET
0.267 0.267 0.267 rg
26.625 329.028 107.042 0.750 re f
26.625 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 319.173 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
132.917 329.028 86.991 0.750 re f
132.917 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 319.173 Td /F1 9.8 Tf  [(21.48)] TJ ET
0.267 0.267 0.267 rg
219.158 329.028 49.034 0.750 re f
219.158 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 319.173 Td /F1 9.8 Tf  [(20.19)] TJ ET
0.267 0.267 0.267 rg
267.442 329.028 49.034 0.750 re f
267.442 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 319.173 Td /F1 9.8 Tf  [(14.88)] TJ ET
0.267 0.267 0.267 rg
315.726 329.028 86.991 0.750 re f
315.726 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 319.173 Td /F1 9.8 Tf  [(17.31)] TJ ET
0.267 0.267 0.267 rg
401.967 329.028 84.930 0.750 re f
401.967 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 319.173 Td /F1 9.8 Tf  [(10.99)] TJ ET
0.267 0.267 0.267 rg
486.147 329.028 46.974 0.750 re f
486.147 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 319.173 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 329.028 48.504 0.750 re f
532.371 313.147 0.750 16.631 re f
580.125 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 319.173 Td /F1 9.8 Tf  [(15.25)] TJ ET
0.267 0.267 0.267 rg
26.625 313.147 107.042 0.750 re f
26.625 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 303.292 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
132.917 313.147 86.991 0.750 re f
132.917 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 303.292 Td /F1 9.8 Tf  [(12.47)] TJ ET
0.267 0.267 0.267 rg
219.158 313.147 49.034 0.750 re f
219.158 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 303.292 Td /F1 9.8 Tf  [(10.93)] TJ ET
0.267 0.267 0.267 rg
267.442 313.147 49.034 0.750 re f
267.442 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 303.292 Td /F1 9.8 Tf  [(15.48)] TJ ET
0.267 0.267 0.267 rg
315.726 313.147 86.991 0.750 re f
315.726 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 303.292 Td /F1 9.8 Tf  [(16.03)] TJ ET
0.267 0.267 0.267 rg
401.967 313.147 84.930 0.750 re f
401.967 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 303.292 Td /F1 9.8 Tf  [(23.08)] TJ ET
0.267 0.267 0.267 rg
486.147 313.147 46.974 0.750 re f
486.147 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 303.292 Td /F1 9.8 Tf  [(18.67)] TJ ET
0.267 0.267 0.267 rg
532.371 313.147 48.504 0.750 re f
532.371 297.265 0.750 16.631 re f
580.125 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 303.292 Td /F1 9.8 Tf  [(16.11)] TJ ET
0.267 0.267 0.267 rg
26.625 297.265 107.042 0.750 re f
26.625 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 287.410 Td /F1 9.8 Tf  [(ML\(ClustalW-)] TJ ET
BT 31.875 279.779 Td /F1 9.8 Tf  [(quicktree\) �)] TJ ET
0.267 0.267 0.267 rg
132.917 297.265 86.991 0.750 re f
132.917 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 287.410 Td /F1 9.8 Tf  [(9.47)] TJ ET
0.267 0.267 0.267 rg
219.158 297.265 49.034 0.750 re f
219.158 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 287.410 Td /F1 9.8 Tf  [(11.40)] TJ ET
0.267 0.267 0.267 rg
267.442 297.265 49.034 0.750 re f
267.442 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 287.410 Td /F1 9.8 Tf  [(20.83)] TJ ET
0.267 0.267 0.267 rg
315.726 297.265 86.991 0.750 re f
315.726 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 287.410 Td /F1 9.8 Tf  [(18.59)] TJ ET
0.267 0.267 0.267 rg
401.967 297.265 84.930 0.750 re f
401.967 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 287.410 Td /F1 9.8 Tf  [(28.57)] TJ ET
0.267 0.267 0.267 rg
486.147 297.265 46.974 0.750 re f
486.147 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 287.410 Td /F1 9.8 Tf  [(24.00)] TJ ET
0.267 0.267 0.267 rg
532.371 297.265 48.504 0.750 re f
532.371 273.753 0.750 24.263 re f
580.125 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 287.410 Td /F1 9.8 Tf  [(18.81)] TJ ET
0.267 0.267 0.267 rg
26.625 273.753 107.042 0.750 re f
26.625 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 263.898 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
132.917 273.753 86.991 0.750 re f
132.917 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 263.898 Td /F1 9.8 Tf  [(18.94)] TJ ET
0.267 0.267 0.267 rg
219.158 273.753 49.034 0.750 re f
219.158 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 263.898 Td /F1 9.8 Tf  [(19.71)] TJ ET
0.267 0.267 0.267 rg
267.442 273.753 49.034 0.750 re f
267.442 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 263.898 Td /F1 9.8 Tf  [(22.02)] TJ ET
0.267 0.267 0.267 rg
315.726 273.753 86.991 0.750 re f
315.726 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 263.898 Td /F1 9.8 Tf  [(26.92)] TJ ET
0.267 0.267 0.267 rg
401.967 273.753 84.930 0.750 re f
401.967 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 263.898 Td /F1 9.8 Tf  [(17.58)] TJ ET
0.267 0.267 0.267 rg
486.147 273.753 46.974 0.750 re f
486.147 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 263.898 Td /F1 9.8 Tf  [(8.00)] TJ ET
0.267 0.267 0.267 rg
532.371 273.753 48.504 0.750 re f
532.371 257.872 0.750 16.631 re f
580.125 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 263.898 Td /F1 9.8 Tf  [(18.86)] TJ ET
0.267 0.267 0.267 rg
26.625 257.872 107.042 0.750 re f
26.625 241.990 0.750 16.631 re f
132.917 257.872 86.616 0.750 re f
219.533 257.872 48.284 0.750 re f
267.817 257.872 48.284 0.750 re f
316.101 257.872 86.241 0.750 re f
402.342 257.872 84.180 0.750 re f
486.522 257.872 46.599 0.750 re f
132.917 241.990 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 248.017 Td /F4 9.8 Tf  [(Alignment SP-FN error \(%\))] TJ ET
0.267 0.267 0.267 rg
532.371 257.872 48.504 0.750 re f
532.371 241.990 0.750 16.631 re f
580.125 241.990 0.750 16.631 re f
26.625 241.990 107.042 0.750 re f
26.625 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 232.135 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
132.917 241.990 86.991 0.750 re f
132.917 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 232.135 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
219.158 241.990 49.034 0.750 re f
219.158 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 232.135 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
267.442 241.990 49.034 0.750 re f
267.442 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 232.135 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
315.726 241.990 86.991 0.750 re f
315.726 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 232.135 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
401.967 241.990 84.930 0.750 re f
401.967 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 232.135 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
486.147 241.990 46.974 0.750 re f
486.147 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 232.135 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
532.371 241.990 48.504 0.750 re f
532.371 218.478 0.750 24.263 re f
580.125 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 232.135 Td /F1 9.8 Tf  [(Avg )] TJ ET
BT 537.621 224.504 Td /F1 9.8 Tf  [(error)] TJ ET
0.267 0.267 0.267 rg
26.625 218.478 107.042 0.750 re f
26.625 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 208.623 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
132.917 218.478 86.991 0.750 re f
132.917 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 208.623 Td /F1 9.8 Tf  [(22.72)] TJ ET
0.267 0.267 0.267 rg
219.158 218.478 49.034 0.750 re f
219.158 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 208.623 Td /F1 9.8 Tf  [(21.98)] TJ ET
0.267 0.267 0.267 rg
267.442 218.478 49.034 0.750 re f
267.442 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 208.623 Td /F1 9.8 Tf  [(29.29)] TJ ET
0.267 0.267 0.267 rg
315.726 218.478 86.991 0.750 re f
315.726 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 208.623 Td /F1 9.8 Tf  [(28.42)] TJ ET
0.267 0.267 0.267 rg
401.967 218.478 84.930 0.750 re f
401.967 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 208.623 Td /F1 9.8 Tf  [(22.15)] TJ ET
0.267 0.267 0.267 rg
486.147 218.478 46.974 0.750 re f
486.147 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 208.623 Td /F1 9.8 Tf  [(21.16)] TJ ET
0.267 0.267 0.267 rg
532.371 218.478 48.504 0.750 re f
532.371 202.597 0.750 16.631 re f
580.125 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 208.623 Td /F1 9.8 Tf  [(24.3)] TJ ET
0.267 0.267 0.267 rg
26.625 202.597 107.042 0.750 re f
26.625 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 192.742 Td /F1 9.8 Tf  [(MAFFT)] TJ ET
0.267 0.267 0.267 rg
132.917 202.597 86.991 0.750 re f
132.917 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 192.742 Td /F1 9.8 Tf  [(22.59)] TJ ET
0.267 0.267 0.267 rg
219.158 202.597 49.034 0.750 re f
219.158 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 192.742 Td /F1 9.8 Tf  [(21.79)] TJ ET
0.267 0.267 0.267 rg
267.442 202.597 49.034 0.750 re f
267.442 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 192.742 Td /F1 9.8 Tf  [(28.61)] TJ ET
0.267 0.267 0.267 rg
315.726 202.597 86.991 0.750 re f
315.726 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 192.742 Td /F1 9.8 Tf  [(28.26)] TJ ET
0.267 0.267 0.267 rg
401.967 202.597 84.930 0.750 re f
401.967 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 192.742 Td /F1 9.8 Tf  [(19.46)] TJ ET
0.267 0.267 0.267 rg
486.147 202.597 46.974 0.750 re f
486.147 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 192.742 Td /F1 9.8 Tf  [(18.48)] TJ ET
0.267 0.267 0.267 rg
532.371 202.597 48.504 0.750 re f
532.371 186.715 0.750 16.631 re f
580.125 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 192.742 Td /F1 9.8 Tf  [(23.2)] TJ ET
0.267 0.267 0.267 rg
26.625 186.715 107.042 0.750 re f
26.625 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 176.860 Td /F1 9.8 Tf  [(MAFFT-PartTree)] TJ ET
0.267 0.267 0.267 rg
132.917 186.715 86.991 0.750 re f
132.917 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 176.860 Td /F1 9.8 Tf  [(23.09)] TJ ET
0.267 0.267 0.267 rg
219.158 186.715 49.034 0.750 re f
219.158 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 176.860 Td /F1 9.8 Tf  [(27.49)] TJ ET
0.267 0.267 0.267 rg
267.442 186.715 49.034 0.750 re f
267.442 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 176.860 Td /F1 9.8 Tf  [(32.11)] TJ ET
0.267 0.267 0.267 rg
315.726 186.715 86.991 0.750 re f
315.726 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 176.860 Td /F1 9.8 Tf  [(33.85)] TJ ET
0.267 0.267 0.267 rg
401.967 186.715 84.930 0.750 re f
401.967 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 176.860 Td /F1 9.8 Tf  [(20.66)] TJ ET
0.267 0.267 0.267 rg
486.147 186.715 46.974 0.750 re f
486.147 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 176.860 Td /F1 9.8 Tf  [(19.65)] TJ ET
0.267 0.267 0.267 rg
532.371 186.715 48.504 0.750 re f
532.371 170.834 0.750 16.631 re f
580.125 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 176.860 Td /F1 9.8 Tf  [(26.1)] TJ ET
0.267 0.267 0.267 rg
26.625 170.834 107.042 0.750 re f
26.625 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 160.979 Td /F1 9.8 Tf  [(Prank+GT)] TJ ET
0.267 0.267 0.267 rg
132.917 170.834 86.991 0.750 re f
132.917 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 160.979 Td /F1 9.8 Tf  [(40.73)] TJ ET
0.267 0.267 0.267 rg
219.158 170.834 49.034 0.750 re f
219.158 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 160.979 Td /F1 9.8 Tf  [(42.40)] TJ ET
0.267 0.267 0.267 rg
267.442 170.834 49.034 0.750 re f
267.442 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 160.979 Td /F1 9.8 Tf  [(44.93)] TJ ET
0.267 0.267 0.267 rg
315.726 170.834 86.991 0.750 re f
315.726 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 160.979 Td /F1 9.8 Tf  [(44.06)] TJ ET
0.267 0.267 0.267 rg
401.967 170.834 84.930 0.750 re f
401.967 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 160.979 Td /F1 9.8 Tf  [(37.32)] TJ ET
0.267 0.267 0.267 rg
486.147 170.834 46.974 0.750 re f
486.147 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 160.979 Td /F1 9.8 Tf  [(35.52)] TJ ET
0.267 0.267 0.267 rg
532.371 170.834 48.504 0.750 re f
532.371 154.953 0.750 16.631 re f
580.125 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 160.979 Td /F1 9.8 Tf  [(40.8)] TJ ET
0.267 0.267 0.267 rg
26.625 154.953 107.042 0.750 re f
26.625 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 145.098 Td /F1 9.8 Tf  [(Muscle)] TJ ET
0.267 0.267 0.267 rg
132.917 154.953 86.991 0.750 re f
132.917 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 145.098 Td /F1 9.8 Tf  [(31.14)] TJ ET
0.267 0.267 0.267 rg
219.158 154.953 49.034 0.750 re f
219.158 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 145.098 Td /F1 9.8 Tf  [(32.02)] TJ ET
0.267 0.267 0.267 rg
267.442 154.953 49.034 0.750 re f
267.442 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 145.098 Td /F1 9.8 Tf  [(34.46)] TJ ET
0.267 0.267 0.267 rg
315.726 154.953 86.991 0.750 re f
315.726 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 145.098 Td /F1 9.8 Tf  [(35.59)] TJ ET
0.267 0.267 0.267 rg
401.967 154.953 84.930 0.750 re f
401.967 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 145.098 Td /F1 9.8 Tf  [(22.79)] TJ ET
0.267 0.267 0.267 rg
486.147 154.953 46.974 0.750 re f
486.147 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 145.098 Td /F1 9.8 Tf  [(21.46)] TJ ET
0.267 0.267 0.267 rg
532.371 154.953 48.504 0.750 re f
532.371 139.072 0.750 16.631 re f
580.125 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 145.098 Td /F1 9.8 Tf  [(29.6)] TJ ET
0.267 0.267 0.267 rg
26.625 139.072 107.042 0.750 re f
26.625 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 129.217 Td /F1 9.8 Tf  [(ClustalW)] TJ ET
0.267 0.267 0.267 rg
132.917 139.072 86.991 0.750 re f
132.917 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 129.217 Td /F1 9.8 Tf  [(38.22)] TJ ET
0.267 0.267 0.267 rg
219.158 139.072 49.034 0.750 re f
219.158 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 129.217 Td /F1 9.8 Tf  [(42.58)] TJ ET
0.267 0.267 0.267 rg
267.442 139.072 49.034 0.750 re f
267.442 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 129.217 Td /F1 9.8 Tf  [(46.25)] TJ ET
0.267 0.267 0.267 rg
315.726 139.072 86.991 0.750 re f
315.726 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 129.217 Td /F1 9.8 Tf  [(47.65)] TJ ET
0.267 0.267 0.267 rg
401.967 139.072 84.930 0.750 re f
401.967 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 129.217 Td /F1 9.8 Tf  [(29.96)] TJ ET
0.267 0.267 0.267 rg
486.147 139.072 46.974 0.750 re f
486.147 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 129.217 Td /F1 9.8 Tf  [(38.54)] TJ ET
0.267 0.267 0.267 rg
532.371 139.072 48.504 0.750 re f
532.371 123.190 0.750 16.631 re f
580.125 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 129.217 Td /F1 9.8 Tf  [(40.5)] TJ ET
0.267 0.267 0.267 rg
26.625 123.190 107.042 0.750 re f
26.625 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 113.335 Td /F1 9.8 Tf  [(ClustalW-quicktree)] TJ ET
0.267 0.267 0.267 rg
132.917 123.190 86.991 0.750 re f
132.917 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 113.335 Td /F1 9.8 Tf  [(37.49)] TJ ET
0.267 0.267 0.267 rg
219.158 123.190 49.034 0.750 re f
219.158 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 113.335 Td /F1 9.8 Tf  [(40.96)] TJ ET
0.267 0.267 0.267 rg
267.442 123.190 49.034 0.750 re f
267.442 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 113.335 Td /F1 9.8 Tf  [(48.38)] TJ ET
0.267 0.267 0.267 rg
315.726 123.190 86.991 0.750 re f
315.726 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 113.335 Td /F1 9.8 Tf  [(43.84)] TJ ET
0.267 0.267 0.267 rg
401.967 123.190 84.930 0.750 re f
401.967 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 113.335 Td /F1 9.8 Tf  [(26.57)] TJ ET
0.267 0.267 0.267 rg
486.147 123.190 46.974 0.750 re f
486.147 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 113.335 Td /F1 9.8 Tf  [(28.07)] TJ ET
0.267 0.267 0.267 rg
532.371 123.190 48.504 0.750 re f
532.371 107.309 0.750 16.631 re f
580.125 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 113.335 Td /F1 9.8 Tf  [(37.6)] TJ ET
0.267 0.267 0.267 rg
26.625 107.309 107.042 0.750 re f
26.625 91.428 107.042 0.750 re f
26.625 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 97.454 Td /F1 9.8 Tf  [(Opal)] TJ ET
0.267 0.267 0.267 rg
132.917 107.309 86.991 0.750 re f
132.917 91.428 86.991 0.750 re f
132.917 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 97.454 Td /F1 9.8 Tf  [(27.71)] TJ ET
0.267 0.267 0.267 rg
219.158 107.309 49.034 0.750 re f
219.158 91.428 49.034 0.750 re f
219.158 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 97.454 Td /F1 9.8 Tf  [(32.36)] TJ ET
0.267 0.267 0.267 rg
267.442 107.309 49.034 0.750 re f
267.442 91.428 49.034 0.750 re f
267.442 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 97.454 Td /F1 9.8 Tf  [(32.22)] TJ ET
0.267 0.267 0.267 rg
315.726 107.309 86.991 0.750 re f
315.726 91.428 86.991 0.750 re f
315.726 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 97.454 Td /F1 9.8 Tf  [(35.01)] TJ ET
0.267 0.267 0.267 rg
401.967 107.309 84.930 0.750 re f
401.967 91.428 84.930 0.750 re f
401.967 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 97.454 Td /F1 9.8 Tf  [(26.64)] TJ ET
0.267 0.267 0.267 rg
486.147 107.309 46.974 0.750 re f
486.147 91.428 46.974 0.750 re f
486.147 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 97.454 Td /F1 9.8 Tf  [(21.61)] TJ ET
0.267 0.267 0.267 rg
532.371 107.309 48.504 0.750 re f
532.371 91.428 48.504 0.750 re f
532.371 91.428 0.750 16.631 re f
580.125 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 97.454 Td /F1 9.8 Tf  [(29.3)] TJ ET
BT 26.250 44.029 Td /F4 9.8 Tf  [(Table 3: Runtimes \(in hours\) for each method on the smaller datasets.)] TJ ET
BT 350.243 44.029 Td /F1 9.8 Tf  [( Each row lists results for a method, and each )] TJ ET
Q
q
15.000 29.743 577.500 747.257 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(place at 41.2 and 20.4 hours, respectively. ClustalW and SAT� take much longer: ClustalW uses 506 hours on the 16S.T )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(dataset and 440 hours on the 16S.3 dataset, while SAT� takes 1505.8 hours on the 16S.T dataset and 563.2 hours on the )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(16S.3 dataset. \(The difference in running time for SAT� on these two datasets is because SAT� runs for ten iterations on the )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(16S.T dataset, but only five iterations on the 16S.3 dataset.\) Maximum likelihood analyses of the four alignment methods that )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(completed on these two datasets were also computationally intensive: on the 16S.T dataset, RAxML analyses ranged from 121 )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(to 156 hours \(depending on the alignment\), while on the 16S.3 dataset, these analyses ranged from 55 to 91 hours. We were )] TJ ET
BT 26.250 696.048 Td /F1 9.8 Tf  [(able to run SAT� successfuly on the 16S.T and 16S.3 datasets using machines with 32 GB main memory available for each )] TJ ET
BT 26.250 684.143 Td /F1 9.8 Tf  [(run, whereas MAFFT and Opal both were unable to analyze the 16S.T dataset on a machine with 32 GB main memory )] TJ ET
BT 26.250 672.238 Td /F1 9.8 Tf  [(available for each run and failed on the 16S.3 dataset.)] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(The Price 78K dataset is the largest of these datasets, and so presents a particularly difficult challenge to the alignment )] TJ ET
BT 26.250 640.929 Td /F1 9.8 Tf  [(methods. On the other hand, the model condition under which this dataset was generated produced a very low number of indels )] TJ ET
BT 26.250 629.024 Td /F1 9.8 Tf  [(\(0.6% of the true matrix is occupied by gaps, two orders of magnitude smaller than what we see for the biological datasets\). )] TJ ET
BT 26.250 617.119 Td /F1 9.8 Tf  [(Therefore, the Price 78K dataset represents primarily a scalability test � i.e., can the alignment method be run on this dataset? � )] TJ ET
BT 26.250 605.214 Td /F1 9.8 Tf  [(rather than a test of accuracy for the resultant alignment. Because of the failures of most alignment methods on the 16S.B.ALL )] TJ ET
BT 26.250 593.310 Td /F1 9.8 Tf  [(dataset, we only attempted to run the Quicktree and PartTree alignments on the Price 78K dataset. Quicktree failed on this )] TJ ET
BT 26.250 581.405 Td /F1 9.8 Tf  [(dataset, but PartTree completed. PartTree used 71.5 hours to complete on this dataset \(less than it used on the 16S.B.ALL )] TJ ET
BT 26.250 569.500 Td /F1 9.8 Tf  [(dataset\). We used FastTree to compute an ML tree on the PartTree alignment, which produced a tree with 9.14% missing )] TJ ET
BT 26.250 557.595 Td /F1 9.8 Tf  [(branch rate in 2.9 hours. While this is a fairly high error rate, by comparison, FastTree on the true alignment \(which took 3.7 )] TJ ET
BT 26.250 545.691 Td /F1 9.8 Tf  [(hours to complete\) had 8% missing branch rate. Since the true alignment has a relatively low number of sites \(1287\) for the )] TJ ET
BT 26.250 533.786 Td /F1 9.8 Tf  [(large number of leaves \(78,132\), it seems likely that the 8% of the edges missing in the FastTree analysis of the true alignment )] TJ ET
BT 26.250 521.881 Td /F1 9.8 Tf  [(are weakly supported. Therefore, the FastTree analysis of the PartTree alignment of the Price 78K dataset is actually highly )] TJ ET
BT 26.250 509.976 Td /F1 9.8 Tf  [(accurate.)] TJ ET
BT 26.250 490.572 Td /F4 9.8 Tf  [(Table 2: Comparison of missing branch rates and alignment SP-FN errors on the six smallest datasets. )] TJ ET
BT 504.683 490.572 Td /F1 9.8 Tf  [( Each row gives )] TJ ET
BT 26.250 478.667 Td /F1 9.8 Tf  [(results for a method, and each column corresponds to a dataset. All analyses succeeded using a dedicated computing core with )] TJ ET
BT 26.250 466.762 Td /F1 9.8 Tf  [(dedicated access to at least 512 MB and at most 4 GB of main memory. The Appendix provides further details about the )] TJ ET
BT 26.250 454.857 Td /F1 9.8 Tf  [(hardware used for these computations. Missing branch rates \(%\) are with respect to the reference tree. Alignment SP-FN errors )] TJ ET
BT 26.250 442.953 Td /F1 9.8 Tf  [(\(%\) are with respect to the curated alignment. ML tree estimation was performed using RAxML.)] TJ ET
1.000 1.000 1.000 rg
26.250 91.053 555.000 342.019 re f
0.267 0.267 0.267 rg
26.625 431.947 107.042 0.750 re f
26.625 416.065 0.750 16.631 re f
132.917 431.947 86.616 0.750 re f
219.533 431.947 48.284 0.750 re f
267.817 431.947 48.284 0.750 re f
316.101 431.947 86.241 0.750 re f
402.342 431.947 84.180 0.750 re f
486.522 431.947 46.599 0.750 re f
132.917 416.065 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 422.092 Td /F4 9.8 Tf  [(Missing branch rate \(%\))] TJ ET
0.267 0.267 0.267 rg
532.371 431.947 48.504 0.750 re f
532.371 416.065 0.750 16.631 re f
580.125 416.065 0.750 16.631 re f
26.625 416.065 107.042 0.750 re f
26.625 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 406.210 Td /F1 9.8 Tf  [(Method)] TJ ET
0.267 0.267 0.267 rg
132.917 416.065 86.991 0.750 re f
132.917 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 406.210 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
219.158 416.065 49.034 0.750 re f
219.158 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 406.210 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
267.442 416.065 49.034 0.750 re f
267.442 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 406.210 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
315.726 416.065 86.991 0.750 re f
315.726 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 406.210 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
401.967 416.065 84.930 0.750 re f
401.967 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 406.210 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
486.147 416.065 46.974 0.750 re f
486.147 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 406.210 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
532.371 416.065 48.504 0.750 re f
532.371 392.553 0.750 24.263 re f
580.125 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 406.210 Td /F1 9.8 Tf  [(Avg )] TJ ET
BT 537.621 398.579 Td /F1 9.8 Tf  [(error)] TJ ET
0.267 0.267 0.267 rg
26.625 392.553 107.042 0.750 re f
26.625 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 382.698 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
132.917 392.553 86.991 0.750 re f
132.917 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 382.698 Td /F1 9.8 Tf  [(5.08)] TJ ET
0.267 0.267 0.267 rg
219.158 392.553 49.034 0.750 re f
219.158 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 382.698 Td /F1 9.8 Tf  [(5.70)] TJ ET
0.267 0.267 0.267 rg
267.442 392.553 49.034 0.750 re f
267.442 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 382.698 Td /F1 9.8 Tf  [(10.12)] TJ ET
0.267 0.267 0.267 rg
315.726 392.553 86.991 0.750 re f
315.726 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 382.698 Td /F1 9.8 Tf  [(10.90)] TJ ET
0.267 0.267 0.267 rg
401.967 392.553 84.930 0.750 re f
401.967 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 382.698 Td /F1 9.8 Tf  [(6.59)] TJ ET
0.267 0.267 0.267 rg
486.147 392.553 46.974 0.750 re f
486.147 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 382.698 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 392.553 48.504 0.750 re f
532.371 376.672 0.750 16.631 re f
580.125 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 382.698 Td /F1 9.8 Tf  [(7.51)] TJ ET
0.267 0.267 0.267 rg
26.625 376.672 107.042 0.750 re f
26.625 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 366.817 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
132.917 376.672 86.991 0.750 re f
132.917 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 366.817 Td /F1 9.8 Tf  [(4.16)] TJ ET
0.267 0.267 0.267 rg
219.158 376.672 49.034 0.750 re f
219.158 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 366.817 Td /F1 9.8 Tf  [(5.70)] TJ ET
0.267 0.267 0.267 rg
267.442 376.672 49.034 0.750 re f
267.442 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 366.817 Td /F1 9.8 Tf  [(11.90)] TJ ET
0.267 0.267 0.267 rg
315.726 376.672 86.991 0.750 re f
315.726 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 366.817 Td /F1 9.8 Tf  [(10.90)] TJ ET
0.267 0.267 0.267 rg
401.967 376.672 84.930 0.750 re f
401.967 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 366.817 Td /F1 9.8 Tf  [(7.69)] TJ ET
0.267 0.267 0.267 rg
486.147 376.672 46.974 0.750 re f
486.147 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 366.817 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 376.672 48.504 0.750 re f
532.371 360.790 0.750 16.631 re f
580.125 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 366.817 Td /F1 9.8 Tf  [(7.84)] TJ ET
0.267 0.267 0.267 rg
26.625 360.790 107.042 0.750 re f
26.625 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 350.935 Td /F1 9.8 Tf  [(ML\(MAFFT-PartTree\))] TJ ET
0.267 0.267 0.267 rg
132.917 360.790 86.991 0.750 re f
132.917 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 350.935 Td /F1 9.8 Tf  [(10.62)] TJ ET
0.267 0.267 0.267 rg
219.158 360.790 49.034 0.750 re f
219.158 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 350.935 Td /F1 9.8 Tf  [(8.79)] TJ ET
0.267 0.267 0.267 rg
267.442 360.790 49.034 0.750 re f
267.442 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 350.935 Td /F1 9.8 Tf  [(22.02)] TJ ET
0.267 0.267 0.267 rg
315.726 360.790 86.991 0.750 re f
315.726 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 350.935 Td /F1 9.8 Tf  [(20.51)] TJ ET
0.267 0.267 0.267 rg
401.967 360.790 84.930 0.750 re f
401.967 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 350.935 Td /F1 9.8 Tf  [(14.29)] TJ ET
0.267 0.267 0.267 rg
486.147 360.790 46.974 0.750 re f
486.147 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 350.935 Td /F1 9.8 Tf  [(5.33)] TJ ET
0.267 0.267 0.267 rg
532.371 360.790 48.504 0.750 re f
532.371 344.909 0.750 16.631 re f
580.125 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 350.935 Td /F1 9.8 Tf  [(13.59)] TJ ET
0.267 0.267 0.267 rg
26.625 344.909 107.042 0.750 re f
26.625 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 335.054 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
132.917 344.909 86.991 0.750 re f
132.917 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 335.054 Td /F1 9.8 Tf  [(7.62)] TJ ET
0.267 0.267 0.267 rg
219.158 344.909 49.034 0.750 re f
219.158 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 335.054 Td /F1 9.8 Tf  [(11.40)] TJ ET
0.267 0.267 0.267 rg
267.442 344.909 49.034 0.750 re f
267.442 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 335.054 Td /F1 9.8 Tf  [(14.29)] TJ ET
0.267 0.267 0.267 rg
315.726 344.909 86.991 0.750 re f
315.726 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 335.054 Td /F1 9.8 Tf  [(19.23)] TJ ET
0.267 0.267 0.267 rg
401.967 344.909 84.930 0.750 re f
401.967 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 335.054 Td /F1 9.8 Tf  [(27.47)] TJ ET
0.267 0.267 0.267 rg
486.147 344.909 46.974 0.750 re f
486.147 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 335.054 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 344.909 48.504 0.750 re f
532.371 329.028 0.750 16.631 re f
580.125 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 335.054 Td /F1 9.8 Tf  [(14.45)] TJ ET
0.267 0.267 0.267 rg
26.625 329.028 107.042 0.750 re f
26.625 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 319.173 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
132.917 329.028 86.991 0.750 re f
132.917 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 319.173 Td /F1 9.8 Tf  [(21.48)] TJ ET
0.267 0.267 0.267 rg
219.158 329.028 49.034 0.750 re f
219.158 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 319.173 Td /F1 9.8 Tf  [(20.19)] TJ ET
0.267 0.267 0.267 rg
267.442 329.028 49.034 0.750 re f
267.442 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 319.173 Td /F1 9.8 Tf  [(14.88)] TJ ET
0.267 0.267 0.267 rg
315.726 329.028 86.991 0.750 re f
315.726 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 319.173 Td /F1 9.8 Tf  [(17.31)] TJ ET
0.267 0.267 0.267 rg
401.967 329.028 84.930 0.750 re f
401.967 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 319.173 Td /F1 9.8 Tf  [(10.99)] TJ ET
0.267 0.267 0.267 rg
486.147 329.028 46.974 0.750 re f
486.147 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 319.173 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 329.028 48.504 0.750 re f
532.371 313.147 0.750 16.631 re f
580.125 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 319.173 Td /F1 9.8 Tf  [(15.25)] TJ ET
0.267 0.267 0.267 rg
26.625 313.147 107.042 0.750 re f
26.625 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 303.292 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
132.917 313.147 86.991 0.750 re f
132.917 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 303.292 Td /F1 9.8 Tf  [(12.47)] TJ ET
0.267 0.267 0.267 rg
219.158 313.147 49.034 0.750 re f
219.158 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 303.292 Td /F1 9.8 Tf  [(10.93)] TJ ET
0.267 0.267 0.267 rg
267.442 313.147 49.034 0.750 re f
267.442 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 303.292 Td /F1 9.8 Tf  [(15.48)] TJ ET
0.267 0.267 0.267 rg
315.726 313.147 86.991 0.750 re f
315.726 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 303.292 Td /F1 9.8 Tf  [(16.03)] TJ ET
0.267 0.267 0.267 rg
401.967 313.147 84.930 0.750 re f
401.967 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 303.292 Td /F1 9.8 Tf  [(23.08)] TJ ET
0.267 0.267 0.267 rg
486.147 313.147 46.974 0.750 re f
486.147 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 303.292 Td /F1 9.8 Tf  [(18.67)] TJ ET
0.267 0.267 0.267 rg
532.371 313.147 48.504 0.750 re f
532.371 297.265 0.750 16.631 re f
580.125 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 303.292 Td /F1 9.8 Tf  [(16.11)] TJ ET
0.267 0.267 0.267 rg
26.625 297.265 107.042 0.750 re f
26.625 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 287.410 Td /F1 9.8 Tf  [(ML\(ClustalW-)] TJ ET
BT 31.875 279.779 Td /F1 9.8 Tf  [(quicktree\) �)] TJ ET
0.267 0.267 0.267 rg
132.917 297.265 86.991 0.750 re f
132.917 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 287.410 Td /F1 9.8 Tf  [(9.47)] TJ ET
0.267 0.267 0.267 rg
219.158 297.265 49.034 0.750 re f
219.158 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 287.410 Td /F1 9.8 Tf  [(11.40)] TJ ET
0.267 0.267 0.267 rg
267.442 297.265 49.034 0.750 re f
267.442 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 287.410 Td /F1 9.8 Tf  [(20.83)] TJ ET
0.267 0.267 0.267 rg
315.726 297.265 86.991 0.750 re f
315.726 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 287.410 Td /F1 9.8 Tf  [(18.59)] TJ ET
0.267 0.267 0.267 rg
401.967 297.265 84.930 0.750 re f
401.967 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 287.410 Td /F1 9.8 Tf  [(28.57)] TJ ET
0.267 0.267 0.267 rg
486.147 297.265 46.974 0.750 re f
486.147 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 287.410 Td /F1 9.8 Tf  [(24.00)] TJ ET
0.267 0.267 0.267 rg
532.371 297.265 48.504 0.750 re f
532.371 273.753 0.750 24.263 re f
580.125 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 287.410 Td /F1 9.8 Tf  [(18.81)] TJ ET
0.267 0.267 0.267 rg
26.625 273.753 107.042 0.750 re f
26.625 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 263.898 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
132.917 273.753 86.991 0.750 re f
132.917 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 263.898 Td /F1 9.8 Tf  [(18.94)] TJ ET
0.267 0.267 0.267 rg
219.158 273.753 49.034 0.750 re f
219.158 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 263.898 Td /F1 9.8 Tf  [(19.71)] TJ ET
0.267 0.267 0.267 rg
267.442 273.753 49.034 0.750 re f
267.442 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 263.898 Td /F1 9.8 Tf  [(22.02)] TJ ET
0.267 0.267 0.267 rg
315.726 273.753 86.991 0.750 re f
315.726 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 263.898 Td /F1 9.8 Tf  [(26.92)] TJ ET
0.267 0.267 0.267 rg
401.967 273.753 84.930 0.750 re f
401.967 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 263.898 Td /F1 9.8 Tf  [(17.58)] TJ ET
0.267 0.267 0.267 rg
486.147 273.753 46.974 0.750 re f
486.147 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 263.898 Td /F1 9.8 Tf  [(8.00)] TJ ET
0.267 0.267 0.267 rg
532.371 273.753 48.504 0.750 re f
532.371 257.872 0.750 16.631 re f
580.125 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 263.898 Td /F1 9.8 Tf  [(18.86)] TJ ET
0.267 0.267 0.267 rg
26.625 257.872 107.042 0.750 re f
26.625 241.990 0.750 16.631 re f
132.917 257.872 86.616 0.750 re f
219.533 257.872 48.284 0.750 re f
267.817 257.872 48.284 0.750 re f
316.101 257.872 86.241 0.750 re f
402.342 257.872 84.180 0.750 re f
486.522 257.872 46.599 0.750 re f
132.917 241.990 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 248.017 Td /F4 9.8 Tf  [(Alignment SP-FN error \(%\))] TJ ET
0.267 0.267 0.267 rg
532.371 257.872 48.504 0.750 re f
532.371 241.990 0.750 16.631 re f
580.125 241.990 0.750 16.631 re f
26.625 241.990 107.042 0.750 re f
26.625 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 232.135 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
132.917 241.990 86.991 0.750 re f
132.917 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 232.135 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
219.158 241.990 49.034 0.750 re f
219.158 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 232.135 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
267.442 241.990 49.034 0.750 re f
267.442 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 232.135 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
315.726 241.990 86.991 0.750 re f
315.726 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 232.135 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
401.967 241.990 84.930 0.750 re f
401.967 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 232.135 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
486.147 241.990 46.974 0.750 re f
486.147 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 232.135 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
532.371 241.990 48.504 0.750 re f
532.371 218.478 0.750 24.263 re f
580.125 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 232.135 Td /F1 9.8 Tf  [(Avg )] TJ ET
BT 537.621 224.504 Td /F1 9.8 Tf  [(error)] TJ ET
0.267 0.267 0.267 rg
26.625 218.478 107.042 0.750 re f
26.625 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 208.623 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
132.917 218.478 86.991 0.750 re f
132.917 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 208.623 Td /F1 9.8 Tf  [(22.72)] TJ ET
0.267 0.267 0.267 rg
219.158 218.478 49.034 0.750 re f
219.158 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 208.623 Td /F1 9.8 Tf  [(21.98)] TJ ET
0.267 0.267 0.267 rg
267.442 218.478 49.034 0.750 re f
267.442 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 208.623 Td /F1 9.8 Tf  [(29.29)] TJ ET
0.267 0.267 0.267 rg
315.726 218.478 86.991 0.750 re f
315.726 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 208.623 Td /F1 9.8 Tf  [(28.42)] TJ ET
0.267 0.267 0.267 rg
401.967 218.478 84.930 0.750 re f
401.967 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 208.623 Td /F1 9.8 Tf  [(22.15)] TJ ET
0.267 0.267 0.267 rg
486.147 218.478 46.974 0.750 re f
486.147 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 208.623 Td /F1 9.8 Tf  [(21.16)] TJ ET
0.267 0.267 0.267 rg
532.371 218.478 48.504 0.750 re f
532.371 202.597 0.750 16.631 re f
580.125 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 208.623 Td /F1 9.8 Tf  [(24.3)] TJ ET
0.267 0.267 0.267 rg
26.625 202.597 107.042 0.750 re f
26.625 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 192.742 Td /F1 9.8 Tf  [(MAFFT)] TJ ET
0.267 0.267 0.267 rg
132.917 202.597 86.991 0.750 re f
132.917 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 192.742 Td /F1 9.8 Tf  [(22.59)] TJ ET
0.267 0.267 0.267 rg
219.158 202.597 49.034 0.750 re f
219.158 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 192.742 Td /F1 9.8 Tf  [(21.79)] TJ ET
0.267 0.267 0.267 rg
267.442 202.597 49.034 0.750 re f
267.442 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 192.742 Td /F1 9.8 Tf  [(28.61)] TJ ET
0.267 0.267 0.267 rg
315.726 202.597 86.991 0.750 re f
315.726 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 192.742 Td /F1 9.8 Tf  [(28.26)] TJ ET
0.267 0.267 0.267 rg
401.967 202.597 84.930 0.750 re f
401.967 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 192.742 Td /F1 9.8 Tf  [(19.46)] TJ ET
0.267 0.267 0.267 rg
486.147 202.597 46.974 0.750 re f
486.147 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 192.742 Td /F1 9.8 Tf  [(18.48)] TJ ET
0.267 0.267 0.267 rg
532.371 202.597 48.504 0.750 re f
532.371 186.715 0.750 16.631 re f
580.125 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 192.742 Td /F1 9.8 Tf  [(23.2)] TJ ET
0.267 0.267 0.267 rg
26.625 186.715 107.042 0.750 re f
26.625 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 176.860 Td /F1 9.8 Tf  [(MAFFT-PartTree)] TJ ET
0.267 0.267 0.267 rg
132.917 186.715 86.991 0.750 re f
132.917 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 176.860 Td /F1 9.8 Tf  [(23.09)] TJ ET
0.267 0.267 0.267 rg
219.158 186.715 49.034 0.750 re f
219.158 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 176.860 Td /F1 9.8 Tf  [(27.49)] TJ ET
0.267 0.267 0.267 rg
267.442 186.715 49.034 0.750 re f
267.442 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 176.860 Td /F1 9.8 Tf  [(32.11)] TJ ET
0.267 0.267 0.267 rg
315.726 186.715 86.991 0.750 re f
315.726 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 176.860 Td /F1 9.8 Tf  [(33.85)] TJ ET
0.267 0.267 0.267 rg
401.967 186.715 84.930 0.750 re f
401.967 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 176.860 Td /F1 9.8 Tf  [(20.66)] TJ ET
0.267 0.267 0.267 rg
486.147 186.715 46.974 0.750 re f
486.147 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 176.860 Td /F1 9.8 Tf  [(19.65)] TJ ET
0.267 0.267 0.267 rg
532.371 186.715 48.504 0.750 re f
532.371 170.834 0.750 16.631 re f
580.125 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 176.860 Td /F1 9.8 Tf  [(26.1)] TJ ET
0.267 0.267 0.267 rg
26.625 170.834 107.042 0.750 re f
26.625 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 160.979 Td /F1 9.8 Tf  [(Prank+GT)] TJ ET
0.267 0.267 0.267 rg
132.917 170.834 86.991 0.750 re f
132.917 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 160.979 Td /F1 9.8 Tf  [(40.73)] TJ ET
0.267 0.267 0.267 rg
219.158 170.834 49.034 0.750 re f
219.158 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 160.979 Td /F1 9.8 Tf  [(42.40)] TJ ET
0.267 0.267 0.267 rg
267.442 170.834 49.034 0.750 re f
267.442 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 160.979 Td /F1 9.8 Tf  [(44.93)] TJ ET
0.267 0.267 0.267 rg
315.726 170.834 86.991 0.750 re f
315.726 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 160.979 Td /F1 9.8 Tf  [(44.06)] TJ ET
0.267 0.267 0.267 rg
401.967 170.834 84.930 0.750 re f
401.967 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 160.979 Td /F1 9.8 Tf  [(37.32)] TJ ET
0.267 0.267 0.267 rg
486.147 170.834 46.974 0.750 re f
486.147 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 160.979 Td /F1 9.8 Tf  [(35.52)] TJ ET
0.267 0.267 0.267 rg
532.371 170.834 48.504 0.750 re f
532.371 154.953 0.750 16.631 re f
580.125 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 160.979 Td /F1 9.8 Tf  [(40.8)] TJ ET
0.267 0.267 0.267 rg
26.625 154.953 107.042 0.750 re f
26.625 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 145.098 Td /F1 9.8 Tf  [(Muscle)] TJ ET
0.267 0.267 0.267 rg
132.917 154.953 86.991 0.750 re f
132.917 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 145.098 Td /F1 9.8 Tf  [(31.14)] TJ ET
0.267 0.267 0.267 rg
219.158 154.953 49.034 0.750 re f
219.158 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 145.098 Td /F1 9.8 Tf  [(32.02)] TJ ET
0.267 0.267 0.267 rg
267.442 154.953 49.034 0.750 re f
267.442 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 145.098 Td /F1 9.8 Tf  [(34.46)] TJ ET
0.267 0.267 0.267 rg
315.726 154.953 86.991 0.750 re f
315.726 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 145.098 Td /F1 9.8 Tf  [(35.59)] TJ ET
0.267 0.267 0.267 rg
401.967 154.953 84.930 0.750 re f
401.967 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 145.098 Td /F1 9.8 Tf  [(22.79)] TJ ET
0.267 0.267 0.267 rg
486.147 154.953 46.974 0.750 re f
486.147 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 145.098 Td /F1 9.8 Tf  [(21.46)] TJ ET
0.267 0.267 0.267 rg
532.371 154.953 48.504 0.750 re f
532.371 139.072 0.750 16.631 re f
580.125 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 145.098 Td /F1 9.8 Tf  [(29.6)] TJ ET
0.267 0.267 0.267 rg
26.625 139.072 107.042 0.750 re f
26.625 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 129.217 Td /F1 9.8 Tf  [(ClustalW)] TJ ET
0.267 0.267 0.267 rg
132.917 139.072 86.991 0.750 re f
132.917 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 129.217 Td /F1 9.8 Tf  [(38.22)] TJ ET
0.267 0.267 0.267 rg
219.158 139.072 49.034 0.750 re f
219.158 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 129.217 Td /F1 9.8 Tf  [(42.58)] TJ ET
0.267 0.267 0.267 rg
267.442 139.072 49.034 0.750 re f
267.442 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 129.217 Td /F1 9.8 Tf  [(46.25)] TJ ET
0.267 0.267 0.267 rg
315.726 139.072 86.991 0.750 re f
315.726 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 129.217 Td /F1 9.8 Tf  [(47.65)] TJ ET
0.267 0.267 0.267 rg
401.967 139.072 84.930 0.750 re f
401.967 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 129.217 Td /F1 9.8 Tf  [(29.96)] TJ ET
0.267 0.267 0.267 rg
486.147 139.072 46.974 0.750 re f
486.147 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 129.217 Td /F1 9.8 Tf  [(38.54)] TJ ET
0.267 0.267 0.267 rg
532.371 139.072 48.504 0.750 re f
532.371 123.190 0.750 16.631 re f
580.125 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 129.217 Td /F1 9.8 Tf  [(40.5)] TJ ET
0.267 0.267 0.267 rg
26.625 123.190 107.042 0.750 re f
26.625 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 113.335 Td /F1 9.8 Tf  [(ClustalW-quicktree)] TJ ET
0.267 0.267 0.267 rg
132.917 123.190 86.991 0.750 re f
132.917 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 113.335 Td /F1 9.8 Tf  [(37.49)] TJ ET
0.267 0.267 0.267 rg
219.158 123.190 49.034 0.750 re f
219.158 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 113.335 Td /F1 9.8 Tf  [(40.96)] TJ ET
0.267 0.267 0.267 rg
267.442 123.190 49.034 0.750 re f
267.442 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 113.335 Td /F1 9.8 Tf  [(48.38)] TJ ET
0.267 0.267 0.267 rg
315.726 123.190 86.991 0.750 re f
315.726 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 113.335 Td /F1 9.8 Tf  [(43.84)] TJ ET
0.267 0.267 0.267 rg
401.967 123.190 84.930 0.750 re f
401.967 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 113.335 Td /F1 9.8 Tf  [(26.57)] TJ ET
0.267 0.267 0.267 rg
486.147 123.190 46.974 0.750 re f
486.147 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 113.335 Td /F1 9.8 Tf  [(28.07)] TJ ET
0.267 0.267 0.267 rg
532.371 123.190 48.504 0.750 re f
532.371 107.309 0.750 16.631 re f
580.125 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 113.335 Td /F1 9.8 Tf  [(37.6)] TJ ET
0.267 0.267 0.267 rg
26.625 107.309 107.042 0.750 re f
26.625 91.428 107.042 0.750 re f
26.625 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 97.454 Td /F1 9.8 Tf  [(Opal)] TJ ET
0.267 0.267 0.267 rg
132.917 107.309 86.991 0.750 re f
132.917 91.428 86.991 0.750 re f
132.917 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 97.454 Td /F1 9.8 Tf  [(27.71)] TJ ET
0.267 0.267 0.267 rg
219.158 107.309 49.034 0.750 re f
219.158 91.428 49.034 0.750 re f
219.158 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 97.454 Td /F1 9.8 Tf  [(32.36)] TJ ET
0.267 0.267 0.267 rg
267.442 107.309 49.034 0.750 re f
267.442 91.428 49.034 0.750 re f
267.442 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 97.454 Td /F1 9.8 Tf  [(32.22)] TJ ET
0.267 0.267 0.267 rg
315.726 107.309 86.991 0.750 re f
315.726 91.428 86.991 0.750 re f
315.726 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 97.454 Td /F1 9.8 Tf  [(35.01)] TJ ET
0.267 0.267 0.267 rg
401.967 107.309 84.930 0.750 re f
401.967 91.428 84.930 0.750 re f
401.967 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 97.454 Td /F1 9.8 Tf  [(26.64)] TJ ET
0.267 0.267 0.267 rg
486.147 107.309 46.974 0.750 re f
486.147 91.428 46.974 0.750 re f
486.147 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 97.454 Td /F1 9.8 Tf  [(21.61)] TJ ET
0.267 0.267 0.267 rg
532.371 107.309 48.504 0.750 re f
532.371 91.428 48.504 0.750 re f
532.371 91.428 0.750 16.631 re f
580.125 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 97.454 Td /F1 9.8 Tf  [(29.3)] TJ ET
BT 26.250 44.029 Td /F4 9.8 Tf  [(Table 3: Runtimes \(in hours\) for each method on the smaller datasets.)] TJ ET
BT 350.243 44.029 Td /F1 9.8 Tf  [( Each row lists results for a method, and each )] TJ ET
Q
q
15.000 29.743 577.500 747.257 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(place at 41.2 and 20.4 hours, respectively. ClustalW and SAT� take much longer: ClustalW uses 506 hours on the 16S.T )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(dataset and 440 hours on the 16S.3 dataset, while SAT� takes 1505.8 hours on the 16S.T dataset and 563.2 hours on the )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(16S.3 dataset. \(The difference in running time for SAT� on these two datasets is because SAT� runs for ten iterations on the )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(16S.T dataset, but only five iterations on the 16S.3 dataset.\) Maximum likelihood analyses of the four alignment methods that )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(completed on these two datasets were also computationally intensive: on the 16S.T dataset, RAxML analyses ranged from 121 )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(to 156 hours \(depending on the alignment\), while on the 16S.3 dataset, these analyses ranged from 55 to 91 hours. We were )] TJ ET
BT 26.250 696.048 Td /F1 9.8 Tf  [(able to run SAT� successfuly on the 16S.T and 16S.3 datasets using machines with 32 GB main memory available for each )] TJ ET
BT 26.250 684.143 Td /F1 9.8 Tf  [(run, whereas MAFFT and Opal both were unable to analyze the 16S.T dataset on a machine with 32 GB main memory )] TJ ET
BT 26.250 672.238 Td /F1 9.8 Tf  [(available for each run and failed on the 16S.3 dataset.)] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(The Price 78K dataset is the largest of these datasets, and so presents a particularly difficult challenge to the alignment )] TJ ET
BT 26.250 640.929 Td /F1 9.8 Tf  [(methods. On the other hand, the model condition under which this dataset was generated produced a very low number of indels )] TJ ET
BT 26.250 629.024 Td /F1 9.8 Tf  [(\(0.6% of the true matrix is occupied by gaps, two orders of magnitude smaller than what we see for the biological datasets\). )] TJ ET
BT 26.250 617.119 Td /F1 9.8 Tf  [(Therefore, the Price 78K dataset represents primarily a scalability test � i.e., can the alignment method be run on this dataset? � )] TJ ET
BT 26.250 605.214 Td /F1 9.8 Tf  [(rather than a test of accuracy for the resultant alignment. Because of the failures of most alignment methods on the 16S.B.ALL )] TJ ET
BT 26.250 593.310 Td /F1 9.8 Tf  [(dataset, we only attempted to run the Quicktree and PartTree alignments on the Price 78K dataset. Quicktree failed on this )] TJ ET
BT 26.250 581.405 Td /F1 9.8 Tf  [(dataset, but PartTree completed. PartTree used 71.5 hours to complete on this dataset \(less than it used on the 16S.B.ALL )] TJ ET
BT 26.250 569.500 Td /F1 9.8 Tf  [(dataset\). We used FastTree to compute an ML tree on the PartTree alignment, which produced a tree with 9.14% missing )] TJ ET
BT 26.250 557.595 Td /F1 9.8 Tf  [(branch rate in 2.9 hours. While this is a fairly high error rate, by comparison, FastTree on the true alignment \(which took 3.7 )] TJ ET
BT 26.250 545.691 Td /F1 9.8 Tf  [(hours to complete\) had 8% missing branch rate. Since the true alignment has a relatively low number of sites \(1287\) for the )] TJ ET
BT 26.250 533.786 Td /F1 9.8 Tf  [(large number of leaves \(78,132\), it seems likely that the 8% of the edges missing in the FastTree analysis of the true alignment )] TJ ET
BT 26.250 521.881 Td /F1 9.8 Tf  [(are weakly supported. Therefore, the FastTree analysis of the PartTree alignment of the Price 78K dataset is actually highly )] TJ ET
BT 26.250 509.976 Td /F1 9.8 Tf  [(accurate.)] TJ ET
BT 26.250 490.572 Td /F4 9.8 Tf  [(Table 2: Comparison of missing branch rates and alignment SP-FN errors on the six smallest datasets. )] TJ ET
BT 504.683 490.572 Td /F1 9.8 Tf  [( Each row gives )] TJ ET
BT 26.250 478.667 Td /F1 9.8 Tf  [(results for a method, and each column corresponds to a dataset. All analyses succeeded using a dedicated computing core with )] TJ ET
BT 26.250 466.762 Td /F1 9.8 Tf  [(dedicated access to at least 512 MB and at most 4 GB of main memory. The Appendix provides further details about the )] TJ ET
BT 26.250 454.857 Td /F1 9.8 Tf  [(hardware used for these computations. Missing branch rates \(%\) are with respect to the reference tree. Alignment SP-FN errors )] TJ ET
BT 26.250 442.953 Td /F1 9.8 Tf  [(\(%\) are with respect to the curated alignment. ML tree estimation was performed using RAxML.)] TJ ET
1.000 1.000 1.000 rg
26.250 91.053 555.000 342.019 re f
0.267 0.267 0.267 rg
26.625 431.947 107.042 0.750 re f
26.625 416.065 0.750 16.631 re f
132.917 431.947 86.616 0.750 re f
219.533 431.947 48.284 0.750 re f
267.817 431.947 48.284 0.750 re f
316.101 431.947 86.241 0.750 re f
402.342 431.947 84.180 0.750 re f
486.522 431.947 46.599 0.750 re f
132.917 416.065 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 422.092 Td /F4 9.8 Tf  [(Missing branch rate \(%\))] TJ ET
0.267 0.267 0.267 rg
532.371 431.947 48.504 0.750 re f
532.371 416.065 0.750 16.631 re f
580.125 416.065 0.750 16.631 re f
26.625 416.065 107.042 0.750 re f
26.625 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 406.210 Td /F1 9.8 Tf  [(Method)] TJ ET
0.267 0.267 0.267 rg
132.917 416.065 86.991 0.750 re f
132.917 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 406.210 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
219.158 416.065 49.034 0.750 re f
219.158 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 406.210 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
267.442 416.065 49.034 0.750 re f
267.442 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 406.210 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
315.726 416.065 86.991 0.750 re f
315.726 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 406.210 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
401.967 416.065 84.930 0.750 re f
401.967 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 406.210 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
486.147 416.065 46.974 0.750 re f
486.147 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 406.210 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
532.371 416.065 48.504 0.750 re f
532.371 392.553 0.750 24.263 re f
580.125 392.553 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 406.210 Td /F1 9.8 Tf  [(Avg )] TJ ET
BT 537.621 398.579 Td /F1 9.8 Tf  [(error)] TJ ET
0.267 0.267 0.267 rg
26.625 392.553 107.042 0.750 re f
26.625 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 382.698 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
132.917 392.553 86.991 0.750 re f
132.917 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 382.698 Td /F1 9.8 Tf  [(5.08)] TJ ET
0.267 0.267 0.267 rg
219.158 392.553 49.034 0.750 re f
219.158 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 382.698 Td /F1 9.8 Tf  [(5.70)] TJ ET
0.267 0.267 0.267 rg
267.442 392.553 49.034 0.750 re f
267.442 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 382.698 Td /F1 9.8 Tf  [(10.12)] TJ ET
0.267 0.267 0.267 rg
315.726 392.553 86.991 0.750 re f
315.726 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 382.698 Td /F1 9.8 Tf  [(10.90)] TJ ET
0.267 0.267 0.267 rg
401.967 392.553 84.930 0.750 re f
401.967 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 382.698 Td /F1 9.8 Tf  [(6.59)] TJ ET
0.267 0.267 0.267 rg
486.147 392.553 46.974 0.750 re f
486.147 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 382.698 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 392.553 48.504 0.750 re f
532.371 376.672 0.750 16.631 re f
580.125 376.672 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 382.698 Td /F1 9.8 Tf  [(7.51)] TJ ET
0.267 0.267 0.267 rg
26.625 376.672 107.042 0.750 re f
26.625 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 366.817 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
132.917 376.672 86.991 0.750 re f
132.917 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 366.817 Td /F1 9.8 Tf  [(4.16)] TJ ET
0.267 0.267 0.267 rg
219.158 376.672 49.034 0.750 re f
219.158 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 366.817 Td /F1 9.8 Tf  [(5.70)] TJ ET
0.267 0.267 0.267 rg
267.442 376.672 49.034 0.750 re f
267.442 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 366.817 Td /F1 9.8 Tf  [(11.90)] TJ ET
0.267 0.267 0.267 rg
315.726 376.672 86.991 0.750 re f
315.726 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 366.817 Td /F1 9.8 Tf  [(10.90)] TJ ET
0.267 0.267 0.267 rg
401.967 376.672 84.930 0.750 re f
401.967 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 366.817 Td /F1 9.8 Tf  [(7.69)] TJ ET
0.267 0.267 0.267 rg
486.147 376.672 46.974 0.750 re f
486.147 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 366.817 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 376.672 48.504 0.750 re f
532.371 360.790 0.750 16.631 re f
580.125 360.790 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 366.817 Td /F1 9.8 Tf  [(7.84)] TJ ET
0.267 0.267 0.267 rg
26.625 360.790 107.042 0.750 re f
26.625 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 350.935 Td /F1 9.8 Tf  [(ML\(MAFFT-PartTree\))] TJ ET
0.267 0.267 0.267 rg
132.917 360.790 86.991 0.750 re f
132.917 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 350.935 Td /F1 9.8 Tf  [(10.62)] TJ ET
0.267 0.267 0.267 rg
219.158 360.790 49.034 0.750 re f
219.158 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 350.935 Td /F1 9.8 Tf  [(8.79)] TJ ET
0.267 0.267 0.267 rg
267.442 360.790 49.034 0.750 re f
267.442 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 350.935 Td /F1 9.8 Tf  [(22.02)] TJ ET
0.267 0.267 0.267 rg
315.726 360.790 86.991 0.750 re f
315.726 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 350.935 Td /F1 9.8 Tf  [(20.51)] TJ ET
0.267 0.267 0.267 rg
401.967 360.790 84.930 0.750 re f
401.967 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 350.935 Td /F1 9.8 Tf  [(14.29)] TJ ET
0.267 0.267 0.267 rg
486.147 360.790 46.974 0.750 re f
486.147 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 350.935 Td /F1 9.8 Tf  [(5.33)] TJ ET
0.267 0.267 0.267 rg
532.371 360.790 48.504 0.750 re f
532.371 344.909 0.750 16.631 re f
580.125 344.909 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 350.935 Td /F1 9.8 Tf  [(13.59)] TJ ET
0.267 0.267 0.267 rg
26.625 344.909 107.042 0.750 re f
26.625 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 335.054 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
132.917 344.909 86.991 0.750 re f
132.917 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 335.054 Td /F1 9.8 Tf  [(7.62)] TJ ET
0.267 0.267 0.267 rg
219.158 344.909 49.034 0.750 re f
219.158 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 335.054 Td /F1 9.8 Tf  [(11.40)] TJ ET
0.267 0.267 0.267 rg
267.442 344.909 49.034 0.750 re f
267.442 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 335.054 Td /F1 9.8 Tf  [(14.29)] TJ ET
0.267 0.267 0.267 rg
315.726 344.909 86.991 0.750 re f
315.726 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 335.054 Td /F1 9.8 Tf  [(19.23)] TJ ET
0.267 0.267 0.267 rg
401.967 344.909 84.930 0.750 re f
401.967 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 335.054 Td /F1 9.8 Tf  [(27.47)] TJ ET
0.267 0.267 0.267 rg
486.147 344.909 46.974 0.750 re f
486.147 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 335.054 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 344.909 48.504 0.750 re f
532.371 329.028 0.750 16.631 re f
580.125 329.028 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 335.054 Td /F1 9.8 Tf  [(14.45)] TJ ET
0.267 0.267 0.267 rg
26.625 329.028 107.042 0.750 re f
26.625 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 319.173 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
132.917 329.028 86.991 0.750 re f
132.917 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 319.173 Td /F1 9.8 Tf  [(21.48)] TJ ET
0.267 0.267 0.267 rg
219.158 329.028 49.034 0.750 re f
219.158 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 319.173 Td /F1 9.8 Tf  [(20.19)] TJ ET
0.267 0.267 0.267 rg
267.442 329.028 49.034 0.750 re f
267.442 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 319.173 Td /F1 9.8 Tf  [(14.88)] TJ ET
0.267 0.267 0.267 rg
315.726 329.028 86.991 0.750 re f
315.726 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 319.173 Td /F1 9.8 Tf  [(17.31)] TJ ET
0.267 0.267 0.267 rg
401.967 329.028 84.930 0.750 re f
401.967 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 319.173 Td /F1 9.8 Tf  [(10.99)] TJ ET
0.267 0.267 0.267 rg
486.147 329.028 46.974 0.750 re f
486.147 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 319.173 Td /F1 9.8 Tf  [(6.67)] TJ ET
0.267 0.267 0.267 rg
532.371 329.028 48.504 0.750 re f
532.371 313.147 0.750 16.631 re f
580.125 313.147 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 319.173 Td /F1 9.8 Tf  [(15.25)] TJ ET
0.267 0.267 0.267 rg
26.625 313.147 107.042 0.750 re f
26.625 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 303.292 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
132.917 313.147 86.991 0.750 re f
132.917 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 303.292 Td /F1 9.8 Tf  [(12.47)] TJ ET
0.267 0.267 0.267 rg
219.158 313.147 49.034 0.750 re f
219.158 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 303.292 Td /F1 9.8 Tf  [(10.93)] TJ ET
0.267 0.267 0.267 rg
267.442 313.147 49.034 0.750 re f
267.442 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 303.292 Td /F1 9.8 Tf  [(15.48)] TJ ET
0.267 0.267 0.267 rg
315.726 313.147 86.991 0.750 re f
315.726 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 303.292 Td /F1 9.8 Tf  [(16.03)] TJ ET
0.267 0.267 0.267 rg
401.967 313.147 84.930 0.750 re f
401.967 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 303.292 Td /F1 9.8 Tf  [(23.08)] TJ ET
0.267 0.267 0.267 rg
486.147 313.147 46.974 0.750 re f
486.147 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 303.292 Td /F1 9.8 Tf  [(18.67)] TJ ET
0.267 0.267 0.267 rg
532.371 313.147 48.504 0.750 re f
532.371 297.265 0.750 16.631 re f
580.125 297.265 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 303.292 Td /F1 9.8 Tf  [(16.11)] TJ ET
0.267 0.267 0.267 rg
26.625 297.265 107.042 0.750 re f
26.625 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 287.410 Td /F1 9.8 Tf  [(ML\(ClustalW-)] TJ ET
BT 31.875 279.779 Td /F1 9.8 Tf  [(quicktree\) �)] TJ ET
0.267 0.267 0.267 rg
132.917 297.265 86.991 0.750 re f
132.917 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 287.410 Td /F1 9.8 Tf  [(9.47)] TJ ET
0.267 0.267 0.267 rg
219.158 297.265 49.034 0.750 re f
219.158 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 287.410 Td /F1 9.8 Tf  [(11.40)] TJ ET
0.267 0.267 0.267 rg
267.442 297.265 49.034 0.750 re f
267.442 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 287.410 Td /F1 9.8 Tf  [(20.83)] TJ ET
0.267 0.267 0.267 rg
315.726 297.265 86.991 0.750 re f
315.726 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 287.410 Td /F1 9.8 Tf  [(18.59)] TJ ET
0.267 0.267 0.267 rg
401.967 297.265 84.930 0.750 re f
401.967 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 287.410 Td /F1 9.8 Tf  [(28.57)] TJ ET
0.267 0.267 0.267 rg
486.147 297.265 46.974 0.750 re f
486.147 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 287.410 Td /F1 9.8 Tf  [(24.00)] TJ ET
0.267 0.267 0.267 rg
532.371 297.265 48.504 0.750 re f
532.371 273.753 0.750 24.263 re f
580.125 273.753 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 287.410 Td /F1 9.8 Tf  [(18.81)] TJ ET
0.267 0.267 0.267 rg
26.625 273.753 107.042 0.750 re f
26.625 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 263.898 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
132.917 273.753 86.991 0.750 re f
132.917 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 263.898 Td /F1 9.8 Tf  [(18.94)] TJ ET
0.267 0.267 0.267 rg
219.158 273.753 49.034 0.750 re f
219.158 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 263.898 Td /F1 9.8 Tf  [(19.71)] TJ ET
0.267 0.267 0.267 rg
267.442 273.753 49.034 0.750 re f
267.442 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 263.898 Td /F1 9.8 Tf  [(22.02)] TJ ET
0.267 0.267 0.267 rg
315.726 273.753 86.991 0.750 re f
315.726 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 263.898 Td /F1 9.8 Tf  [(26.92)] TJ ET
0.267 0.267 0.267 rg
401.967 273.753 84.930 0.750 re f
401.967 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 263.898 Td /F1 9.8 Tf  [(17.58)] TJ ET
0.267 0.267 0.267 rg
486.147 273.753 46.974 0.750 re f
486.147 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 263.898 Td /F1 9.8 Tf  [(8.00)] TJ ET
0.267 0.267 0.267 rg
532.371 273.753 48.504 0.750 re f
532.371 257.872 0.750 16.631 re f
580.125 257.872 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 263.898 Td /F1 9.8 Tf  [(18.86)] TJ ET
0.267 0.267 0.267 rg
26.625 257.872 107.042 0.750 re f
26.625 241.990 0.750 16.631 re f
132.917 257.872 86.616 0.750 re f
219.533 257.872 48.284 0.750 re f
267.817 257.872 48.284 0.750 re f
316.101 257.872 86.241 0.750 re f
402.342 257.872 84.180 0.750 re f
486.522 257.872 46.599 0.750 re f
132.917 241.990 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 248.017 Td /F4 9.8 Tf  [(Alignment SP-FN error \(%\))] TJ ET
0.267 0.267 0.267 rg
532.371 257.872 48.504 0.750 re f
532.371 241.990 0.750 16.631 re f
580.125 241.990 0.750 16.631 re f
26.625 241.990 107.042 0.750 re f
26.625 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 232.135 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
132.917 241.990 86.991 0.750 re f
132.917 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 138.167 232.135 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
219.158 241.990 49.034 0.750 re f
219.158 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 224.408 232.135 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
267.442 241.990 49.034 0.750 re f
267.442 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 272.692 232.135 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
315.726 241.990 86.991 0.750 re f
315.726 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 320.976 232.135 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
401.967 241.990 84.930 0.750 re f
401.967 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 407.217 232.135 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
486.147 241.990 46.974 0.750 re f
486.147 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 491.397 232.135 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
532.371 241.990 48.504 0.750 re f
532.371 218.478 0.750 24.263 re f
580.125 218.478 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 537.621 232.135 Td /F1 9.8 Tf  [(Avg )] TJ ET
BT 537.621 224.504 Td /F1 9.8 Tf  [(error)] TJ ET
0.267 0.267 0.267 rg
26.625 218.478 107.042 0.750 re f
26.625 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 208.623 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
132.917 218.478 86.991 0.750 re f
132.917 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 208.623 Td /F1 9.8 Tf  [(22.72)] TJ ET
0.267 0.267 0.267 rg
219.158 218.478 49.034 0.750 re f
219.158 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 208.623 Td /F1 9.8 Tf  [(21.98)] TJ ET
0.267 0.267 0.267 rg
267.442 218.478 49.034 0.750 re f
267.442 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 208.623 Td /F1 9.8 Tf  [(29.29)] TJ ET
0.267 0.267 0.267 rg
315.726 218.478 86.991 0.750 re f
315.726 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 208.623 Td /F1 9.8 Tf  [(28.42)] TJ ET
0.267 0.267 0.267 rg
401.967 218.478 84.930 0.750 re f
401.967 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 208.623 Td /F1 9.8 Tf  [(22.15)] TJ ET
0.267 0.267 0.267 rg
486.147 218.478 46.974 0.750 re f
486.147 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 208.623 Td /F1 9.8 Tf  [(21.16)] TJ ET
0.267 0.267 0.267 rg
532.371 218.478 48.504 0.750 re f
532.371 202.597 0.750 16.631 re f
580.125 202.597 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 208.623 Td /F1 9.8 Tf  [(24.3)] TJ ET
0.267 0.267 0.267 rg
26.625 202.597 107.042 0.750 re f
26.625 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 192.742 Td /F1 9.8 Tf  [(MAFFT)] TJ ET
0.267 0.267 0.267 rg
132.917 202.597 86.991 0.750 re f
132.917 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 192.742 Td /F1 9.8 Tf  [(22.59)] TJ ET
0.267 0.267 0.267 rg
219.158 202.597 49.034 0.750 re f
219.158 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 192.742 Td /F1 9.8 Tf  [(21.79)] TJ ET
0.267 0.267 0.267 rg
267.442 202.597 49.034 0.750 re f
267.442 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 192.742 Td /F1 9.8 Tf  [(28.61)] TJ ET
0.267 0.267 0.267 rg
315.726 202.597 86.991 0.750 re f
315.726 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 192.742 Td /F1 9.8 Tf  [(28.26)] TJ ET
0.267 0.267 0.267 rg
401.967 202.597 84.930 0.750 re f
401.967 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 192.742 Td /F1 9.8 Tf  [(19.46)] TJ ET
0.267 0.267 0.267 rg
486.147 202.597 46.974 0.750 re f
486.147 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 192.742 Td /F1 9.8 Tf  [(18.48)] TJ ET
0.267 0.267 0.267 rg
532.371 202.597 48.504 0.750 re f
532.371 186.715 0.750 16.631 re f
580.125 186.715 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 192.742 Td /F1 9.8 Tf  [(23.2)] TJ ET
0.267 0.267 0.267 rg
26.625 186.715 107.042 0.750 re f
26.625 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 176.860 Td /F1 9.8 Tf  [(MAFFT-PartTree)] TJ ET
0.267 0.267 0.267 rg
132.917 186.715 86.991 0.750 re f
132.917 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 176.860 Td /F1 9.8 Tf  [(23.09)] TJ ET
0.267 0.267 0.267 rg
219.158 186.715 49.034 0.750 re f
219.158 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 176.860 Td /F1 9.8 Tf  [(27.49)] TJ ET
0.267 0.267 0.267 rg
267.442 186.715 49.034 0.750 re f
267.442 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 176.860 Td /F1 9.8 Tf  [(32.11)] TJ ET
0.267 0.267 0.267 rg
315.726 186.715 86.991 0.750 re f
315.726 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 176.860 Td /F1 9.8 Tf  [(33.85)] TJ ET
0.267 0.267 0.267 rg
401.967 186.715 84.930 0.750 re f
401.967 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 176.860 Td /F1 9.8 Tf  [(20.66)] TJ ET
0.267 0.267 0.267 rg
486.147 186.715 46.974 0.750 re f
486.147 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 176.860 Td /F1 9.8 Tf  [(19.65)] TJ ET
0.267 0.267 0.267 rg
532.371 186.715 48.504 0.750 re f
532.371 170.834 0.750 16.631 re f
580.125 170.834 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 176.860 Td /F1 9.8 Tf  [(26.1)] TJ ET
0.267 0.267 0.267 rg
26.625 170.834 107.042 0.750 re f
26.625 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 160.979 Td /F1 9.8 Tf  [(Prank+GT)] TJ ET
0.267 0.267 0.267 rg
132.917 170.834 86.991 0.750 re f
132.917 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 160.979 Td /F1 9.8 Tf  [(40.73)] TJ ET
0.267 0.267 0.267 rg
219.158 170.834 49.034 0.750 re f
219.158 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 160.979 Td /F1 9.8 Tf  [(42.40)] TJ ET
0.267 0.267 0.267 rg
267.442 170.834 49.034 0.750 re f
267.442 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 160.979 Td /F1 9.8 Tf  [(44.93)] TJ ET
0.267 0.267 0.267 rg
315.726 170.834 86.991 0.750 re f
315.726 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 160.979 Td /F1 9.8 Tf  [(44.06)] TJ ET
0.267 0.267 0.267 rg
401.967 170.834 84.930 0.750 re f
401.967 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 160.979 Td /F1 9.8 Tf  [(37.32)] TJ ET
0.267 0.267 0.267 rg
486.147 170.834 46.974 0.750 re f
486.147 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 160.979 Td /F1 9.8 Tf  [(35.52)] TJ ET
0.267 0.267 0.267 rg
532.371 170.834 48.504 0.750 re f
532.371 154.953 0.750 16.631 re f
580.125 154.953 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 160.979 Td /F1 9.8 Tf  [(40.8)] TJ ET
0.267 0.267 0.267 rg
26.625 154.953 107.042 0.750 re f
26.625 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 145.098 Td /F1 9.8 Tf  [(Muscle)] TJ ET
0.267 0.267 0.267 rg
132.917 154.953 86.991 0.750 re f
132.917 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 145.098 Td /F1 9.8 Tf  [(31.14)] TJ ET
0.267 0.267 0.267 rg
219.158 154.953 49.034 0.750 re f
219.158 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 145.098 Td /F1 9.8 Tf  [(32.02)] TJ ET
0.267 0.267 0.267 rg
267.442 154.953 49.034 0.750 re f
267.442 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 145.098 Td /F1 9.8 Tf  [(34.46)] TJ ET
0.267 0.267 0.267 rg
315.726 154.953 86.991 0.750 re f
315.726 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 145.098 Td /F1 9.8 Tf  [(35.59)] TJ ET
0.267 0.267 0.267 rg
401.967 154.953 84.930 0.750 re f
401.967 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 145.098 Td /F1 9.8 Tf  [(22.79)] TJ ET
0.267 0.267 0.267 rg
486.147 154.953 46.974 0.750 re f
486.147 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 145.098 Td /F1 9.8 Tf  [(21.46)] TJ ET
0.267 0.267 0.267 rg
532.371 154.953 48.504 0.750 re f
532.371 139.072 0.750 16.631 re f
580.125 139.072 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 145.098 Td /F1 9.8 Tf  [(29.6)] TJ ET
0.267 0.267 0.267 rg
26.625 139.072 107.042 0.750 re f
26.625 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 129.217 Td /F1 9.8 Tf  [(ClustalW)] TJ ET
0.267 0.267 0.267 rg
132.917 139.072 86.991 0.750 re f
132.917 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 129.217 Td /F1 9.8 Tf  [(38.22)] TJ ET
0.267 0.267 0.267 rg
219.158 139.072 49.034 0.750 re f
219.158 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 129.217 Td /F1 9.8 Tf  [(42.58)] TJ ET
0.267 0.267 0.267 rg
267.442 139.072 49.034 0.750 re f
267.442 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 129.217 Td /F1 9.8 Tf  [(46.25)] TJ ET
0.267 0.267 0.267 rg
315.726 139.072 86.991 0.750 re f
315.726 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 129.217 Td /F1 9.8 Tf  [(47.65)] TJ ET
0.267 0.267 0.267 rg
401.967 139.072 84.930 0.750 re f
401.967 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 129.217 Td /F1 9.8 Tf  [(29.96)] TJ ET
0.267 0.267 0.267 rg
486.147 139.072 46.974 0.750 re f
486.147 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 129.217 Td /F1 9.8 Tf  [(38.54)] TJ ET
0.267 0.267 0.267 rg
532.371 139.072 48.504 0.750 re f
532.371 123.190 0.750 16.631 re f
580.125 123.190 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 129.217 Td /F1 9.8 Tf  [(40.5)] TJ ET
0.267 0.267 0.267 rg
26.625 123.190 107.042 0.750 re f
26.625 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 113.335 Td /F1 9.8 Tf  [(ClustalW-quicktree)] TJ ET
0.267 0.267 0.267 rg
132.917 123.190 86.991 0.750 re f
132.917 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 113.335 Td /F1 9.8 Tf  [(37.49)] TJ ET
0.267 0.267 0.267 rg
219.158 123.190 49.034 0.750 re f
219.158 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 113.335 Td /F1 9.8 Tf  [(40.96)] TJ ET
0.267 0.267 0.267 rg
267.442 123.190 49.034 0.750 re f
267.442 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 113.335 Td /F1 9.8 Tf  [(48.38)] TJ ET
0.267 0.267 0.267 rg
315.726 123.190 86.991 0.750 re f
315.726 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 113.335 Td /F1 9.8 Tf  [(43.84)] TJ ET
0.267 0.267 0.267 rg
401.967 123.190 84.930 0.750 re f
401.967 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 113.335 Td /F1 9.8 Tf  [(26.57)] TJ ET
0.267 0.267 0.267 rg
486.147 123.190 46.974 0.750 re f
486.147 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 113.335 Td /F1 9.8 Tf  [(28.07)] TJ ET
0.267 0.267 0.267 rg
532.371 123.190 48.504 0.750 re f
532.371 107.309 0.750 16.631 re f
580.125 107.309 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 113.335 Td /F1 9.8 Tf  [(37.6)] TJ ET
0.267 0.267 0.267 rg
26.625 107.309 107.042 0.750 re f
26.625 91.428 107.042 0.750 re f
26.625 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 97.454 Td /F1 9.8 Tf  [(Opal)] TJ ET
0.267 0.267 0.267 rg
132.917 107.309 86.991 0.750 re f
132.917 91.428 86.991 0.750 re f
132.917 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 138.167 97.454 Td /F1 9.8 Tf  [(27.71)] TJ ET
0.267 0.267 0.267 rg
219.158 107.309 49.034 0.750 re f
219.158 91.428 49.034 0.750 re f
219.158 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.408 97.454 Td /F1 9.8 Tf  [(32.36)] TJ ET
0.267 0.267 0.267 rg
267.442 107.309 49.034 0.750 re f
267.442 91.428 49.034 0.750 re f
267.442 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 272.692 97.454 Td /F1 9.8 Tf  [(32.22)] TJ ET
0.267 0.267 0.267 rg
315.726 107.309 86.991 0.750 re f
315.726 91.428 86.991 0.750 re f
315.726 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 320.976 97.454 Td /F1 9.8 Tf  [(35.01)] TJ ET
0.267 0.267 0.267 rg
401.967 107.309 84.930 0.750 re f
401.967 91.428 84.930 0.750 re f
401.967 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 407.217 97.454 Td /F1 9.8 Tf  [(26.64)] TJ ET
0.267 0.267 0.267 rg
486.147 107.309 46.974 0.750 re f
486.147 91.428 46.974 0.750 re f
486.147 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 491.397 97.454 Td /F1 9.8 Tf  [(21.61)] TJ ET
0.267 0.267 0.267 rg
532.371 107.309 48.504 0.750 re f
532.371 91.428 48.504 0.750 re f
532.371 91.428 0.750 16.631 re f
580.125 91.428 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 537.621 97.454 Td /F1 9.8 Tf  [(29.3)] TJ ET
BT 26.250 44.029 Td /F4 9.8 Tf  [(Table 3: Runtimes \(in hours\) for each method on the smaller datasets.)] TJ ET
BT 350.243 44.029 Td /F1 9.8 Tf  [( Each row lists results for a method, and each )] TJ ET
Q
q
0.000 0.000 0.000 rg
BT 291.710 19.825 Td /F1 11.0 Tf  [(5)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

Q
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0.271 0.267 0.267 rg
q
15.000 71.086 577.500 705.914 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(column corresponds to a dataset. All analyses succeeded using a dedicated computing core with dedicated access to at least )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(512 MB and at most 4 GB of main memory. The Appendix provides further details about the hardware used for these )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(computations. ML tree estimation was performed using RAxML. The runtimes given for SAT� include the initial phase, which )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(includes the calculation of the four two-phase methods, followed by a 24 hour analysis. We do not divide SAT�s runtime into )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(time used for alignment and tree estimation, but just show the total.)] TJ ET
1.000 1.000 1.000 rg
26.250 534.401 555.000 175.575 re f
0.267 0.267 0.267 rg
26.625 708.851 95.498 0.750 re f
26.625 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 698.996 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
121.373 708.851 40.718 0.750 re f
162.092 708.851 40.396 0.750 re f
121.373 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 698.996 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
201.737 708.851 40.718 0.750 re f
242.455 708.851 35.580 0.750 re f
201.737 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 698.996 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
277.286 708.851 37.504 0.750 re f
314.790 708.851 35.580 0.750 re f
277.286 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 698.996 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
349.620 708.851 40.396 0.750 re f
390.016 708.851 40.396 0.750 re f
349.620 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 698.996 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
429.662 708.851 39.440 0.750 re f
469.101 708.851 39.440 0.750 re f
429.662 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 698.996 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
507.791 708.851 37.504 0.750 re f
545.295 708.851 35.580 0.750 re f
507.791 692.970 0.750 16.631 re f
580.125 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 698.996 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
26.625 692.970 95.498 0.750 re f
26.625 677.089 0.750 16.631 re f
121.373 692.970 41.093 0.750 re f
121.373 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
161.717 692.970 40.771 0.750 re f
161.717 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
201.737 692.970 41.093 0.750 re f
201.737 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
242.080 692.970 35.955 0.750 re f
242.080 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
277.286 692.970 37.879 0.750 re f
277.286 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
314.415 692.970 35.955 0.750 re f
314.415 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
349.620 692.970 40.771 0.750 re f
349.620 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
389.641 692.970 40.771 0.750 re f
389.641 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
429.662 692.970 39.815 0.750 re f
429.662 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
468.726 692.970 39.815 0.750 re f
468.726 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
507.791 692.970 37.879 0.750 re f
507.791 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
544.920 692.970 35.955 0.750 re f
544.920 677.089 0.750 16.631 re f
580.125 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
26.625 677.089 95.498 0.750 re f
26.625 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 667.234 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
121.373 677.089 41.093 0.750 re f
121.373 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 667.234 Td /F1 9.8 Tf  [(114.5)] TJ ET
0.267 0.267 0.267 rg
161.717 677.089 40.771 0.750 re f
161.717 661.207 0.750 16.631 re f
201.737 677.089 41.093 0.750 re f
201.737 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 667.234 Td /F1 9.8 Tf  [(106.0)] TJ ET
0.267 0.267 0.267 rg
242.080 677.089 35.955 0.750 re f
242.080 661.207 0.750 16.631 re f
277.286 677.089 37.879 0.750 re f
277.286 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 667.234 Td /F1 9.8 Tf  [(68.9)] TJ ET
0.267 0.267 0.267 rg
314.415 677.089 35.955 0.750 re f
314.415 661.207 0.750 16.631 re f
349.620 677.089 40.771 0.750 re f
349.620 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 667.234 Td /F1 9.8 Tf  [(67.2)] TJ ET
0.267 0.267 0.267 rg
389.641 677.089 40.771 0.750 re f
389.641 661.207 0.750 16.631 re f
429.662 677.089 39.815 0.750 re f
429.662 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 667.234 Td /F1 9.8 Tf  [(61.8)] TJ ET
0.267 0.267 0.267 rg
468.726 677.089 39.815 0.750 re f
468.726 661.207 0.750 16.631 re f
507.791 677.089 37.879 0.750 re f
507.791 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 667.234 Td /F1 9.8 Tf  [(60.0)] TJ ET
0.267 0.267 0.267 rg
544.920 677.089 35.955 0.750 re f
544.920 661.207 0.750 16.631 re f
580.125 661.207 0.750 16.631 re f
26.625 661.207 95.498 0.750 re f
26.625 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 651.353 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
121.373 661.207 41.093 0.750 re f
121.373 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 651.353 Td /F1 9.8 Tf  [(9.2)] TJ ET
0.267 0.267 0.267 rg
161.717 661.207 40.771 0.750 re f
161.717 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 651.353 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
201.737 661.207 41.093 0.750 re f
201.737 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 651.353 Td /F1 9.8 Tf  [(5.8)] TJ ET
0.267 0.267 0.267 rg
242.080 661.207 35.955 0.750 re f
242.080 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 651.353 Td /F1 9.8 Tf  [(3.6)] TJ ET
0.267 0.267 0.267 rg
277.286 661.207 37.879 0.750 re f
277.286 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 651.353 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
314.415 661.207 35.955 0.750 re f
314.415 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 651.353 Td /F1 9.8 Tf  [(2.2)] TJ ET
0.267 0.267 0.267 rg
349.620 661.207 40.771 0.750 re f
349.620 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 651.353 Td /F1 9.8 Tf  [(1.7)] TJ ET
0.267 0.267 0.267 rg
389.641 661.207 40.771 0.750 re f
389.641 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 651.353 Td /F1 9.8 Tf  [(1.1)] TJ ET
0.267 0.267 0.267 rg
429.662 661.207 39.815 0.750 re f
429.662 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 651.353 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
468.726 661.207 39.815 0.750 re f
468.726 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 651.353 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
507.791 661.207 37.879 0.750 re f
507.791 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 651.353 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
544.920 661.207 35.955 0.750 re f
544.920 645.326 0.750 16.631 re f
580.125 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 651.353 Td /F1 9.8 Tf  [(0.3)] TJ ET
0.267 0.267 0.267 rg
26.625 645.326 95.498 0.750 re f
26.625 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 635.471 Td /F1 9.8 Tf  [(ML\(MAFFT-)] TJ ET
BT 31.875 627.840 Td /F1 9.8 Tf  [(PartTree\))] TJ ET
0.267 0.267 0.267 rg
121.373 645.326 41.093 0.750 re f
121.373 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 126.623 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
161.717 645.326 40.771 0.750 re f
161.717 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 166.967 635.471 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
201.737 645.326 41.093 0.750 re f
201.737 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 206.987 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
242.080 645.326 35.955 0.750 re f
242.080 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 247.330 635.471 Td /F1 9.8 Tf  [(6.6)] TJ ET
0.267 0.267 0.267 rg
277.286 645.326 37.879 0.750 re f
277.286 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 282.536 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
314.415 645.326 35.955 0.750 re f
314.415 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 319.665 635.471 Td /F1 9.8 Tf  [(1.9)] TJ ET
0.267 0.267 0.267 rg
349.620 645.326 40.771 0.750 re f
349.620 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 354.870 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
389.641 645.326 40.771 0.750 re f
389.641 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 394.891 635.471 Td /F1 9.8 Tf  [(1.6)] TJ ET
0.267 0.267 0.267 rg
429.662 645.326 39.815 0.750 re f
429.662 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 434.912 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
468.726 645.326 39.815 0.750 re f
468.726 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 473.976 635.471 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
507.791 645.326 37.879 0.750 re f
507.791 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 513.041 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
544.920 645.326 35.955 0.750 re f
544.920 621.814 0.750 24.263 re f
580.125 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 550.170 635.471 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
26.625 621.814 95.498 0.750 re f
26.625 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 611.959 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
121.373 621.814 41.093 0.750 re f
121.373 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 611.959 Td /F1 9.8 Tf  [(15.4)] TJ ET
0.267 0.267 0.267 rg
161.717 621.814 40.771 0.750 re f
161.717 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 611.959 Td /F1 9.8 Tf  [(17.1)] TJ ET
0.267 0.267 0.267 rg
201.737 621.814 41.093 0.750 re f
201.737 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 611.959 Td /F1 9.8 Tf  [(9.7)] TJ ET
0.267 0.267 0.267 rg
242.080 621.814 35.955 0.750 re f
242.080 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 611.959 Td /F1 9.8 Tf  [(12.5)] TJ ET
0.267 0.267 0.267 rg
277.286 621.814 37.879 0.750 re f
277.286 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 611.959 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
314.415 621.814 35.955 0.750 re f
314.415 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 611.959 Td /F1 9.8 Tf  [(3.3)] TJ ET
0.267 0.267 0.267 rg
349.620 621.814 40.771 0.750 re f
349.620 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 611.959 Td /F1 9.8 Tf  [(5.3)] TJ ET
0.267 0.267 0.267 rg
389.641 621.814 40.771 0.750 re f
389.641 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 611.959 Td /F1 9.8 Tf  [(2.6)] TJ ET
0.267 0.267 0.267 rg
429.662 621.814 39.815 0.750 re f
429.662 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 611.959 Td /F1 9.8 Tf  [(8.3)] TJ ET
0.267 0.267 0.267 rg
468.726 621.814 39.815 0.750 re f
468.726 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 611.959 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
507.791 621.814 37.879 0.750 re f
507.791 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 611.959 Td /F1 9.8 Tf  [(7.4)] TJ ET
0.267 0.267 0.267 rg
544.920 621.814 35.955 0.750 re f
544.920 605.933 0.750 16.631 re f
580.125 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 611.959 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
26.625 605.933 95.498 0.750 re f
26.625 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 596.077 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
121.373 605.933 41.093 0.750 re f
121.373 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 596.077 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
161.717 605.933 40.771 0.750 re f
161.717 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 596.077 Td /F1 9.8 Tf  [(6.1)] TJ ET
0.267 0.267 0.267 rg
201.737 605.933 41.093 0.750 re f
201.737 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 596.077 Td /F1 9.8 Tf  [(10.3)] TJ ET
0.267 0.267 0.267 rg
242.080 605.933 35.955 0.750 re f
242.080 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 596.077 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
277.286 605.933 37.879 0.750 re f
277.286 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 596.077 Td /F1 9.8 Tf  [(3.1)] TJ ET
0.267 0.267 0.267 rg
314.415 605.933 35.955 0.750 re f
314.415 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 596.077 Td /F1 9.8 Tf  [(1.1)] TJ ET
0.267 0.267 0.267 rg
349.620 605.933 40.771 0.750 re f
349.620 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 596.077 Td /F1 9.8 Tf  [(2.5)] TJ ET
0.267 0.267 0.267 rg
389.641 605.933 40.771 0.750 re f
389.641 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 596.077 Td /F1 9.8 Tf  [(1.6)] TJ ET
0.267 0.267 0.267 rg
429.662 605.933 39.815 0.750 re f
429.662 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 596.077 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
468.726 605.933 39.815 0.750 re f
468.726 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 596.077 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
507.791 605.933 37.879 0.750 re f
507.791 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 596.077 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
544.920 605.933 35.955 0.750 re f
544.920 590.051 0.750 16.631 re f
580.125 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 596.077 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
26.625 590.051 95.498 0.750 re f
26.625 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 580.196 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
121.373 590.051 41.093 0.750 re f
121.373 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 580.196 Td /F1 9.8 Tf  [(5.6)] TJ ET
0.267 0.267 0.267 rg
161.717 590.051 40.771 0.750 re f
161.717 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 580.196 Td /F1 9.8 Tf  [(4.5)] TJ ET
0.267 0.267 0.267 rg
201.737 590.051 41.093 0.750 re f
201.737 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 580.196 Td /F1 9.8 Tf  [(6.3)] TJ ET
0.267 0.267 0.267 rg
242.080 590.051 35.955 0.750 re f
242.080 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 580.196 Td /F1 9.8 Tf  [(2.5)] TJ ET
0.267 0.267 0.267 rg
277.286 590.051 37.879 0.750 re f
277.286 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 580.196 Td /F1 9.8 Tf  [(1.5)] TJ ET
0.267 0.267 0.267 rg
314.415 590.051 35.955 0.750 re f
314.415 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 580.196 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
349.620 590.051 40.771 0.750 re f
349.620 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 580.196 Td /F1 9.8 Tf  [(1.3)] TJ ET
0.267 0.267 0.267 rg
389.641 590.051 40.771 0.750 re f
389.641 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 580.196 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
429.662 590.051 39.815 0.750 re f
429.662 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 580.196 Td /F1 9.8 Tf  [(2.0)] TJ ET
0.267 0.267 0.267 rg
468.726 590.051 39.815 0.750 re f
468.726 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 580.196 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
507.791 590.051 37.879 0.750 re f
507.791 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 580.196 Td /F1 9.8 Tf  [(1.7)] TJ ET
0.267 0.267 0.267 rg
544.920 590.051 35.955 0.750 re f
544.920 574.170 0.750 16.631 re f
580.125 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 580.196 Td /F1 9.8 Tf  [(0.3)] TJ ET
0.267 0.267 0.267 rg
26.625 574.170 95.498 0.750 re f
26.625 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 564.315 Td /F1 9.8 Tf  [(ML\(ClustalW-)] TJ ET
BT 31.875 556.684 Td /F1 9.8 Tf  [(quicktree\))] TJ ET
0.267 0.267 0.267 rg
121.373 574.170 41.093 0.750 re f
121.373 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 126.623 564.315 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
161.717 574.170 40.771 0.750 re f
161.717 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 166.967 564.315 Td /F1 9.8 Tf  [(4.3)] TJ ET
0.267 0.267 0.267 rg
201.737 574.170 41.093 0.750 re f
201.737 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 206.987 564.315 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
242.080 574.170 35.955 0.750 re f
242.080 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 247.330 564.315 Td /F1 9.8 Tf  [(3.6)] TJ ET
0.267 0.267 0.267 rg
277.286 574.170 37.879 0.750 re f
277.286 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 282.536 564.315 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
314.415 574.170 35.955 0.750 re f
314.415 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 319.665 564.315 Td /F1 9.8 Tf  [(1.5)] TJ ET
0.267 0.267 0.267 rg
349.620 574.170 40.771 0.750 re f
349.620 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 354.870 564.315 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
389.641 574.170 40.771 0.750 re f
389.641 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 394.891 564.315 Td /F1 9.8 Tf  [(1.2)] TJ ET
0.267 0.267 0.267 rg
429.662 574.170 39.815 0.750 re f
429.662 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 434.912 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
468.726 574.170 39.815 0.750 re f
468.726 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 473.976 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
507.791 574.170 37.879 0.750 re f
507.791 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 513.041 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
544.920 574.170 35.955 0.750 re f
544.920 550.657 0.750 24.263 re f
580.125 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 550.170 564.315 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
26.625 550.657 95.498 0.750 re f
26.625 534.776 95.498 0.750 re f
26.625 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 540.803 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
121.373 550.657 41.093 0.750 re f
121.373 534.776 41.093 0.750 re f
121.373 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 540.803 Td /F1 9.8 Tf  [(3.4)] TJ ET
0.267 0.267 0.267 rg
161.717 550.657 40.771 0.750 re f
161.717 534.776 40.771 0.750 re f
161.717 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 540.803 Td /F1 9.8 Tf  [(14.3)] TJ ET
0.267 0.267 0.267 rg
201.737 550.657 41.093 0.750 re f
201.737 534.776 41.093 0.750 re f
201.737 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 540.803 Td /F1 9.8 Tf  [(3.2)] TJ ET
0.267 0.267 0.267 rg
242.080 550.657 35.955 0.750 re f
242.080 534.776 35.955 0.750 re f
242.080 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 540.803 Td /F1 9.8 Tf  [(8.1)] TJ ET
0.267 0.267 0.267 rg
277.286 550.657 37.879 0.750 re f
277.286 534.776 37.879 0.750 re f
277.286 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 540.803 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
314.415 550.657 35.955 0.750 re f
314.415 534.776 35.955 0.750 re f
314.415 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 540.803 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
349.620 550.657 40.771 0.750 re f
349.620 534.776 40.771 0.750 re f
349.620 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 540.803 Td /F1 9.8 Tf  [(2.1)] TJ ET
0.267 0.267 0.267 rg
389.641 550.657 40.771 0.750 re f
389.641 534.776 40.771 0.750 re f
389.641 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 540.803 Td /F1 9.8 Tf  [(1.9)] TJ ET
0.267 0.267 0.267 rg
429.662 550.657 39.815 0.750 re f
429.662 534.776 39.815 0.750 re f
429.662 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 540.803 Td /F1 9.8 Tf  [(3.8)] TJ ET
0.267 0.267 0.267 rg
468.726 550.657 39.815 0.750 re f
468.726 534.776 39.815 0.750 re f
468.726 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 540.803 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
507.791 550.657 37.879 0.750 re f
507.791 534.776 37.879 0.750 re f
507.791 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 540.803 Td /F1 9.8 Tf  [(4.1)] TJ ET
0.267 0.267 0.267 rg
544.920 550.657 35.955 0.750 re f
544.920 534.776 35.955 0.750 re f
544.920 534.776 0.750 16.631 re f
580.125 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 540.803 Td /F1 9.8 Tf  [(0.4)] TJ ET
BT 26.250 487.377 Td /F4 9.8 Tf  [(Table 4: Comparison of missing branch rates and alignment SP-FN errors on the four largest datasets.)] TJ ET
BT 500.324 487.377 Td /F1 9.8 Tf  [( Each row lists )] TJ ET
BT 26.250 475.473 Td /F1 9.8 Tf  [(results for a method, and each column corresponds to a dataset. Missing branch rates \(%\) are with respect to the reference )] TJ ET
BT 26.250 463.568 Td /F1 9.8 Tf  [(tree. Alignment SP-FN errors \(%\) are with respect to the reference alignment. ML estimation was performed using RAxML on all )] TJ ET
BT 26.250 451.663 Td /F1 9.8 Tf  [(alignments with the exception of alignments estimated on the Price 78K dataset, for which we used FastTree \(we note this by )] TJ ET
BT 26.250 439.758 Td /F1 9.8 Tf  [(using the prefix �FT:� before the missing branch rate for the Price 78K dataset\). �F� indicates that the method aborted on the )] TJ ET
BT 26.250 427.854 Td /F1 9.8 Tf  [(dataset, and �s.r.� indicates that the method was still running on a 256 GB machine, at the time of submission of this manuscript. )] TJ ET
BT 26.250 415.949 Td /F1 9.8 Tf  [(Entry �n.a.� means �not attempted�; in the case of the results for ML trees produced on estimated alignments, this meant that )] TJ ET
BT 26.250 404.044 Td /F1 9.8 Tf  [(either we did not attempt to run the alignment, or that the alignment estimation did not complete. Entry �n.c.� for alignment SP-)] TJ ET
BT 26.250 392.139 Td /F1 9.8 Tf  [(FN error means �not computed�; this is given for those datasets that are so large that computing the alignment SP-FN error is )] TJ ET
BT 26.250 380.235 Td /F1 9.8 Tf  [(infeasible due to computational challenges. The Appendix provides further details about the hardware used for these )] TJ ET
BT 26.250 368.330 Td /F1 9.8 Tf  [(computations.)] TJ ET
1.000 1.000 1.000 rg
26.250 71.086 555.000 287.363 re f
0.267 0.267 0.267 rg
26.625 357.324 193.482 0.750 re f
26.625 341.443 0.750 16.631 re f
219.357 357.324 98.841 0.750 re f
318.198 357.324 116.090 0.750 re f
434.288 357.324 73.658 0.750 re f
507.946 357.324 72.929 0.750 re f
219.357 341.443 0.750 16.631 re f
580.125 341.443 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 347.469 Td /F4 9.8 Tf  [(Missing branch rate \(%\))] TJ ET
0.267 0.267 0.267 rg
26.625 341.443 193.482 0.750 re f
26.625 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 331.588 Td /F1 9.8 Tf  [(Method)] TJ ET
0.267 0.267 0.267 rg
219.357 341.443 99.216 0.750 re f
219.357 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 331.588 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
317.823 341.443 116.840 0.750 re f
317.823 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 331.588 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
433.913 341.443 74.408 0.750 re f
433.913 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 331.588 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
507.571 341.443 73.304 0.750 re f
507.571 325.562 0.750 16.631 re f
580.125 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 331.588 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
26.625 325.562 193.482 0.750 re f
26.625 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 315.707 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
219.357 325.562 99.216 0.750 re f
219.357 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 315.707 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 325.562 116.840 0.750 re f
317.823 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 315.707 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 325.562 74.408 0.750 re f
433.913 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 315.707 Td /F1 9.8 Tf  [(7.59)] TJ ET
0.267 0.267 0.267 rg
507.571 325.562 73.304 0.750 re f
507.571 309.680 0.750 16.631 re f
580.125 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 315.707 Td /F1 9.8 Tf  [(7.00)] TJ ET
0.267 0.267 0.267 rg
26.625 309.680 193.482 0.750 re f
26.625 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 299.825 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
219.357 309.680 99.216 0.750 re f
219.357 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 299.825 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 309.680 116.840 0.750 re f
317.823 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 299.825 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 309.680 74.408 0.750 re f
433.913 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 299.825 Td /F1 9.8 Tf  [(7.29)] TJ ET
0.267 0.267 0.267 rg
507.571 309.680 73.304 0.750 re f
507.571 293.799 0.750 16.631 re f
580.125 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 299.825 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 293.799 193.482 0.750 re f
26.625 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 283.944 Td /F1 9.8 Tf  [(ML\(MAFFT-PartTree\))] TJ ET
0.267 0.267 0.267 rg
219.357 293.799 99.216 0.750 re f
219.357 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 283.944 Td /F1 9.8 Tf  [(FT:9.14)] TJ ET
0.267 0.267 0.267 rg
317.823 293.799 116.840 0.750 re f
317.823 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 283.944 Td /F1 9.8 Tf  [(32.19)] TJ ET
0.267 0.267 0.267 rg
433.913 293.799 74.408 0.750 re f
433.913 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 283.944 Td /F1 9.8 Tf  [(16.73)] TJ ET
0.267 0.267 0.267 rg
507.571 293.799 73.304 0.750 re f
507.571 277.918 0.750 16.631 re f
580.125 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 283.944 Td /F1 9.8 Tf  [(11.83)] TJ ET
0.267 0.267 0.267 rg
26.625 277.918 193.482 0.750 re f
26.625 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 268.063 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
219.357 277.918 99.216 0.750 re f
219.357 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 268.063 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 277.918 116.840 0.750 re f
317.823 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 268.063 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 277.918 74.408 0.750 re f
433.913 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 268.063 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 277.918 73.304 0.750 re f
507.571 262.037 0.750 16.631 re f
580.125 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 268.063 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 262.037 193.482 0.750 re f
26.625 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 252.182 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
219.357 262.037 99.216 0.750 re f
219.357 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 252.182 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 262.037 116.840 0.750 re f
317.823 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
433.913 262.037 74.408 0.750 re f
433.913 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 262.037 73.304 0.750 re f
507.571 246.155 0.750 16.631 re f
580.125 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
26.625 246.155 193.482 0.750 re f
26.625 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 236.300 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
219.357 246.155 99.216 0.750 re f
219.357 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 236.300 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 246.155 116.840 0.750 re f
317.823 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 236.300 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 246.155 74.408 0.750 re f
433.913 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 236.300 Td /F1 9.8 Tf  [(10.21)] TJ ET
0.267 0.267 0.267 rg
507.571 246.155 73.304 0.750 re f
507.571 230.274 0.750 16.631 re f
580.125 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 236.300 Td /F1 9.8 Tf  [(9.29)] TJ ET
0.267 0.267 0.267 rg
26.625 230.274 193.482 0.750 re f
26.625 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 220.419 Td /F1 9.8 Tf  [(ML\(ClustalW-quicktree\))] TJ ET
0.267 0.267 0.267 rg
219.357 230.274 99.216 0.750 re f
219.357 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 220.419 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
317.823 230.274 116.840 0.750 re f
317.823 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 220.419 Td /F1 9.8 Tf  [(13.07)] TJ ET
0.267 0.267 0.267 rg
433.913 230.274 74.408 0.750 re f
433.913 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 220.419 Td /F1 9.8 Tf  [(34.23)] TJ ET
0.267 0.267 0.267 rg
507.571 230.274 73.304 0.750 re f
507.571 214.393 0.750 16.631 re f
580.125 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 220.419 Td /F1 9.8 Tf  [(31.47)] TJ ET
0.267 0.267 0.267 rg
26.625 214.393 193.482 0.750 re f
26.625 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 204.538 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
219.357 214.393 99.216 0.750 re f
219.357 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 204.538 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 214.393 116.840 0.750 re f
317.823 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 204.538 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 214.393 74.408 0.750 re f
433.913 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 204.538 Td /F1 9.8 Tf  [(18.62)] TJ ET
0.267 0.267 0.267 rg
507.571 214.393 73.304 0.750 re f
507.571 198.511 0.750 16.631 re f
580.125 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 204.538 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 198.511 193.482 0.750 re f
26.625 182.630 0.750 16.631 re f
219.357 198.511 98.841 0.750 re f
318.198 198.511 116.090 0.750 re f
434.288 198.511 73.658 0.750 re f
507.946 198.511 72.929 0.750 re f
219.357 182.630 0.750 16.631 re f
580.125 182.630 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 188.656 Td /F4 9.8 Tf  [(Alignment SP-FN error \(%\))] TJ ET
0.267 0.267 0.267 rg
26.625 182.630 193.482 0.750 re f
26.625 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 172.775 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
219.357 182.630 99.216 0.750 re f
219.357 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 172.775 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
317.823 182.630 116.840 0.750 re f
317.823 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 172.775 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
433.913 182.630 74.408 0.750 re f
433.913 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 172.775 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
507.571 182.630 73.304 0.750 re f
507.571 166.749 0.750 16.631 re f
580.125 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 172.775 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
26.625 166.749 193.482 0.750 re f
26.625 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 156.894 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
219.357 166.749 99.216 0.750 re f
219.357 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 156.894 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 166.749 116.840 0.750 re f
317.823 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 156.894 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 166.749 74.408 0.750 re f
433.913 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 156.894 Td /F1 9.8 Tf  [(36.96)] TJ ET
0.267 0.267 0.267 rg
507.571 166.749 73.304 0.750 re f
507.571 150.868 0.750 16.631 re f
580.125 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 156.894 Td /F1 9.8 Tf  [(24.93)] TJ ET
0.267 0.267 0.267 rg
26.625 150.868 193.482 0.750 re f
26.625 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 141.013 Td /F1 9.8 Tf  [(MAFFT)] TJ ET
0.267 0.267 0.267 rg
219.357 150.868 99.216 0.750 re f
219.357 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 141.013 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 150.868 116.840 0.750 re f
317.823 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 141.013 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 150.868 74.408 0.750 re f
433.913 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 141.013 Td /F1 9.8 Tf  [(30.97)] TJ ET
0.267 0.267 0.267 rg
507.571 150.868 73.304 0.750 re f
507.571 134.986 0.750 16.631 re f
580.125 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 141.013 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 134.986 193.482 0.750 re f
26.625 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 125.131 Td /F1 9.8 Tf  [(MAFFT-PartTree)] TJ ET
0.267 0.267 0.267 rg
219.357 134.986 99.216 0.750 re f
219.357 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 125.131 Td /F1 9.8 Tf  [(n.c.)] TJ ET
0.267 0.267 0.267 rg
317.823 134.986 116.840 0.750 re f
317.823 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 125.131 Td /F1 9.8 Tf  [(41.73)] TJ ET
0.267 0.267 0.267 rg
433.913 134.986 74.408 0.750 re f
433.913 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 125.131 Td /F1 9.8 Tf  [(34.29)] TJ ET
0.267 0.267 0.267 rg
507.571 134.986 73.304 0.750 re f
507.571 119.105 0.750 16.631 re f
580.125 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 125.131 Td /F1 9.8 Tf  [(22.64)] TJ ET
0.267 0.267 0.267 rg
26.625 119.105 193.482 0.750 re f
26.625 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 109.250 Td /F1 9.8 Tf  [(Prank+GT)] TJ ET
0.267 0.267 0.267 rg
219.357 119.105 99.216 0.750 re f
219.357 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 109.250 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 119.105 116.840 0.750 re f
317.823 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 109.250 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 119.105 74.408 0.750 re f
433.913 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 109.250 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 119.105 73.304 0.750 re f
507.571 103.224 0.750 16.631 re f
580.125 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 109.250 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 103.224 193.482 0.750 re f
26.625 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 93.369 Td /F1 9.8 Tf  [(Muscle)] TJ ET
0.267 0.267 0.267 rg
219.357 103.224 99.216 0.750 re f
219.357 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 93.369 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 103.224 116.840 0.750 re f
317.823 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
433.913 103.224 74.408 0.750 re f
433.913 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 103.224 73.304 0.750 re f
507.571 87.343 0.750 16.631 re f
580.125 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
26.625 87.343 193.482 0.750 re f
26.625 71.461 193.482 0.750 re f
26.625 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 77.488 Td /F1 9.8 Tf  [(ClustalW)] TJ ET
0.267 0.267 0.267 rg
219.357 87.343 99.216 0.750 re f
219.357 71.461 99.216 0.750 re f
219.357 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 77.488 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 87.343 116.840 0.750 re f
317.823 71.461 116.840 0.750 re f
317.823 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 77.488 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 87.343 74.408 0.750 re f
433.913 71.461 74.408 0.750 re f
433.913 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 77.488 Td /F1 9.8 Tf  [(56.33)] TJ ET
0.267 0.267 0.267 rg
507.571 87.343 73.304 0.750 re f
507.571 71.461 73.304 0.750 re f
507.571 71.461 0.750 16.631 re f
580.125 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 77.488 Td /F1 9.8 Tf  [(52.04)] TJ ET
Q
q
15.000 71.086 577.500 705.914 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(column corresponds to a dataset. All analyses succeeded using a dedicated computing core with dedicated access to at least )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(512 MB and at most 4 GB of main memory. The Appendix provides further details about the hardware used for these )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(computations. ML tree estimation was performed using RAxML. The runtimes given for SAT� include the initial phase, which )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(includes the calculation of the four two-phase methods, followed by a 24 hour analysis. We do not divide SAT�s runtime into )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(time used for alignment and tree estimation, but just show the total.)] TJ ET
1.000 1.000 1.000 rg
26.250 534.401 555.000 175.575 re f
0.267 0.267 0.267 rg
26.625 708.851 95.498 0.750 re f
26.625 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 698.996 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
121.373 708.851 40.718 0.750 re f
162.092 708.851 40.396 0.750 re f
121.373 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 698.996 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
201.737 708.851 40.718 0.750 re f
242.455 708.851 35.580 0.750 re f
201.737 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 698.996 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
277.286 708.851 37.504 0.750 re f
314.790 708.851 35.580 0.750 re f
277.286 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 698.996 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
349.620 708.851 40.396 0.750 re f
390.016 708.851 40.396 0.750 re f
349.620 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 698.996 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
429.662 708.851 39.440 0.750 re f
469.101 708.851 39.440 0.750 re f
429.662 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 698.996 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
507.791 708.851 37.504 0.750 re f
545.295 708.851 35.580 0.750 re f
507.791 692.970 0.750 16.631 re f
580.125 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 698.996 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
26.625 692.970 95.498 0.750 re f
26.625 677.089 0.750 16.631 re f
121.373 692.970 41.093 0.750 re f
121.373 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
161.717 692.970 40.771 0.750 re f
161.717 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
201.737 692.970 41.093 0.750 re f
201.737 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
242.080 692.970 35.955 0.750 re f
242.080 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
277.286 692.970 37.879 0.750 re f
277.286 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
314.415 692.970 35.955 0.750 re f
314.415 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
349.620 692.970 40.771 0.750 re f
349.620 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
389.641 692.970 40.771 0.750 re f
389.641 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
429.662 692.970 39.815 0.750 re f
429.662 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
468.726 692.970 39.815 0.750 re f
468.726 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
507.791 692.970 37.879 0.750 re f
507.791 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
544.920 692.970 35.955 0.750 re f
544.920 677.089 0.750 16.631 re f
580.125 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
26.625 677.089 95.498 0.750 re f
26.625 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 667.234 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
121.373 677.089 41.093 0.750 re f
121.373 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 667.234 Td /F1 9.8 Tf  [(114.5)] TJ ET
0.267 0.267 0.267 rg
161.717 677.089 40.771 0.750 re f
161.717 661.207 0.750 16.631 re f
201.737 677.089 41.093 0.750 re f
201.737 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 667.234 Td /F1 9.8 Tf  [(106.0)] TJ ET
0.267 0.267 0.267 rg
242.080 677.089 35.955 0.750 re f
242.080 661.207 0.750 16.631 re f
277.286 677.089 37.879 0.750 re f
277.286 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 667.234 Td /F1 9.8 Tf  [(68.9)] TJ ET
0.267 0.267 0.267 rg
314.415 677.089 35.955 0.750 re f
314.415 661.207 0.750 16.631 re f
349.620 677.089 40.771 0.750 re f
349.620 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 667.234 Td /F1 9.8 Tf  [(67.2)] TJ ET
0.267 0.267 0.267 rg
389.641 677.089 40.771 0.750 re f
389.641 661.207 0.750 16.631 re f
429.662 677.089 39.815 0.750 re f
429.662 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 667.234 Td /F1 9.8 Tf  [(61.8)] TJ ET
0.267 0.267 0.267 rg
468.726 677.089 39.815 0.750 re f
468.726 661.207 0.750 16.631 re f
507.791 677.089 37.879 0.750 re f
507.791 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 667.234 Td /F1 9.8 Tf  [(60.0)] TJ ET
0.267 0.267 0.267 rg
544.920 677.089 35.955 0.750 re f
544.920 661.207 0.750 16.631 re f
580.125 661.207 0.750 16.631 re f
26.625 661.207 95.498 0.750 re f
26.625 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 651.353 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
121.373 661.207 41.093 0.750 re f
121.373 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 651.353 Td /F1 9.8 Tf  [(9.2)] TJ ET
0.267 0.267 0.267 rg
161.717 661.207 40.771 0.750 re f
161.717 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 651.353 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
201.737 661.207 41.093 0.750 re f
201.737 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 651.353 Td /F1 9.8 Tf  [(5.8)] TJ ET
0.267 0.267 0.267 rg
242.080 661.207 35.955 0.750 re f
242.080 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 651.353 Td /F1 9.8 Tf  [(3.6)] TJ ET
0.267 0.267 0.267 rg
277.286 661.207 37.879 0.750 re f
277.286 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 651.353 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
314.415 661.207 35.955 0.750 re f
314.415 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 651.353 Td /F1 9.8 Tf  [(2.2)] TJ ET
0.267 0.267 0.267 rg
349.620 661.207 40.771 0.750 re f
349.620 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 651.353 Td /F1 9.8 Tf  [(1.7)] TJ ET
0.267 0.267 0.267 rg
389.641 661.207 40.771 0.750 re f
389.641 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 651.353 Td /F1 9.8 Tf  [(1.1)] TJ ET
0.267 0.267 0.267 rg
429.662 661.207 39.815 0.750 re f
429.662 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 651.353 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
468.726 661.207 39.815 0.750 re f
468.726 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 651.353 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
507.791 661.207 37.879 0.750 re f
507.791 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 651.353 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
544.920 661.207 35.955 0.750 re f
544.920 645.326 0.750 16.631 re f
580.125 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 651.353 Td /F1 9.8 Tf  [(0.3)] TJ ET
0.267 0.267 0.267 rg
26.625 645.326 95.498 0.750 re f
26.625 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 635.471 Td /F1 9.8 Tf  [(ML\(MAFFT-)] TJ ET
BT 31.875 627.840 Td /F1 9.8 Tf  [(PartTree\))] TJ ET
0.267 0.267 0.267 rg
121.373 645.326 41.093 0.750 re f
121.373 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 126.623 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
161.717 645.326 40.771 0.750 re f
161.717 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 166.967 635.471 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
201.737 645.326 41.093 0.750 re f
201.737 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 206.987 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
242.080 645.326 35.955 0.750 re f
242.080 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 247.330 635.471 Td /F1 9.8 Tf  [(6.6)] TJ ET
0.267 0.267 0.267 rg
277.286 645.326 37.879 0.750 re f
277.286 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 282.536 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
314.415 645.326 35.955 0.750 re f
314.415 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 319.665 635.471 Td /F1 9.8 Tf  [(1.9)] TJ ET
0.267 0.267 0.267 rg
349.620 645.326 40.771 0.750 re f
349.620 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 354.870 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
389.641 645.326 40.771 0.750 re f
389.641 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 394.891 635.471 Td /F1 9.8 Tf  [(1.6)] TJ ET
0.267 0.267 0.267 rg
429.662 645.326 39.815 0.750 re f
429.662 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 434.912 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
468.726 645.326 39.815 0.750 re f
468.726 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 473.976 635.471 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
507.791 645.326 37.879 0.750 re f
507.791 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 513.041 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
544.920 645.326 35.955 0.750 re f
544.920 621.814 0.750 24.263 re f
580.125 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 550.170 635.471 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
26.625 621.814 95.498 0.750 re f
26.625 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 611.959 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
121.373 621.814 41.093 0.750 re f
121.373 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 611.959 Td /F1 9.8 Tf  [(15.4)] TJ ET
0.267 0.267 0.267 rg
161.717 621.814 40.771 0.750 re f
161.717 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 611.959 Td /F1 9.8 Tf  [(17.1)] TJ ET
0.267 0.267 0.267 rg
201.737 621.814 41.093 0.750 re f
201.737 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 611.959 Td /F1 9.8 Tf  [(9.7)] TJ ET
0.267 0.267 0.267 rg
242.080 621.814 35.955 0.750 re f
242.080 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 611.959 Td /F1 9.8 Tf  [(12.5)] TJ ET
0.267 0.267 0.267 rg
277.286 621.814 37.879 0.750 re f
277.286 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 611.959 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
314.415 621.814 35.955 0.750 re f
314.415 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 611.959 Td /F1 9.8 Tf  [(3.3)] TJ ET
0.267 0.267 0.267 rg
349.620 621.814 40.771 0.750 re f
349.620 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 611.959 Td /F1 9.8 Tf  [(5.3)] TJ ET
0.267 0.267 0.267 rg
389.641 621.814 40.771 0.750 re f
389.641 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 611.959 Td /F1 9.8 Tf  [(2.6)] TJ ET
0.267 0.267 0.267 rg
429.662 621.814 39.815 0.750 re f
429.662 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 611.959 Td /F1 9.8 Tf  [(8.3)] TJ ET
0.267 0.267 0.267 rg
468.726 621.814 39.815 0.750 re f
468.726 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 611.959 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
507.791 621.814 37.879 0.750 re f
507.791 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 611.959 Td /F1 9.8 Tf  [(7.4)] TJ ET
0.267 0.267 0.267 rg
544.920 621.814 35.955 0.750 re f
544.920 605.933 0.750 16.631 re f
580.125 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 611.959 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
26.625 605.933 95.498 0.750 re f
26.625 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 596.077 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
121.373 605.933 41.093 0.750 re f
121.373 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 596.077 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
161.717 605.933 40.771 0.750 re f
161.717 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 596.077 Td /F1 9.8 Tf  [(6.1)] TJ ET
0.267 0.267 0.267 rg
201.737 605.933 41.093 0.750 re f
201.737 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 596.077 Td /F1 9.8 Tf  [(10.3)] TJ ET
0.267 0.267 0.267 rg
242.080 605.933 35.955 0.750 re f
242.080 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 596.077 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
277.286 605.933 37.879 0.750 re f
277.286 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 596.077 Td /F1 9.8 Tf  [(3.1)] TJ ET
0.267 0.267 0.267 rg
314.415 605.933 35.955 0.750 re f
314.415 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 596.077 Td /F1 9.8 Tf  [(1.1)] TJ ET
0.267 0.267 0.267 rg
349.620 605.933 40.771 0.750 re f
349.620 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 596.077 Td /F1 9.8 Tf  [(2.5)] TJ ET
0.267 0.267 0.267 rg
389.641 605.933 40.771 0.750 re f
389.641 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 596.077 Td /F1 9.8 Tf  [(1.6)] TJ ET
0.267 0.267 0.267 rg
429.662 605.933 39.815 0.750 re f
429.662 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 596.077 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
468.726 605.933 39.815 0.750 re f
468.726 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 596.077 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
507.791 605.933 37.879 0.750 re f
507.791 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 596.077 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
544.920 605.933 35.955 0.750 re f
544.920 590.051 0.750 16.631 re f
580.125 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 596.077 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
26.625 590.051 95.498 0.750 re f
26.625 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 580.196 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
121.373 590.051 41.093 0.750 re f
121.373 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 580.196 Td /F1 9.8 Tf  [(5.6)] TJ ET
0.267 0.267 0.267 rg
161.717 590.051 40.771 0.750 re f
161.717 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 580.196 Td /F1 9.8 Tf  [(4.5)] TJ ET
0.267 0.267 0.267 rg
201.737 590.051 41.093 0.750 re f
201.737 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 580.196 Td /F1 9.8 Tf  [(6.3)] TJ ET
0.267 0.267 0.267 rg
242.080 590.051 35.955 0.750 re f
242.080 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 580.196 Td /F1 9.8 Tf  [(2.5)] TJ ET
0.267 0.267 0.267 rg
277.286 590.051 37.879 0.750 re f
277.286 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 580.196 Td /F1 9.8 Tf  [(1.5)] TJ ET
0.267 0.267 0.267 rg
314.415 590.051 35.955 0.750 re f
314.415 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 580.196 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
349.620 590.051 40.771 0.750 re f
349.620 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 580.196 Td /F1 9.8 Tf  [(1.3)] TJ ET
0.267 0.267 0.267 rg
389.641 590.051 40.771 0.750 re f
389.641 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 580.196 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
429.662 590.051 39.815 0.750 re f
429.662 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 580.196 Td /F1 9.8 Tf  [(2.0)] TJ ET
0.267 0.267 0.267 rg
468.726 590.051 39.815 0.750 re f
468.726 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 580.196 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
507.791 590.051 37.879 0.750 re f
507.791 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 580.196 Td /F1 9.8 Tf  [(1.7)] TJ ET
0.267 0.267 0.267 rg
544.920 590.051 35.955 0.750 re f
544.920 574.170 0.750 16.631 re f
580.125 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 580.196 Td /F1 9.8 Tf  [(0.3)] TJ ET
0.267 0.267 0.267 rg
26.625 574.170 95.498 0.750 re f
26.625 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 564.315 Td /F1 9.8 Tf  [(ML\(ClustalW-)] TJ ET
BT 31.875 556.684 Td /F1 9.8 Tf  [(quicktree\))] TJ ET
0.267 0.267 0.267 rg
121.373 574.170 41.093 0.750 re f
121.373 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 126.623 564.315 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
161.717 574.170 40.771 0.750 re f
161.717 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 166.967 564.315 Td /F1 9.8 Tf  [(4.3)] TJ ET
0.267 0.267 0.267 rg
201.737 574.170 41.093 0.750 re f
201.737 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 206.987 564.315 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
242.080 574.170 35.955 0.750 re f
242.080 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 247.330 564.315 Td /F1 9.8 Tf  [(3.6)] TJ ET
0.267 0.267 0.267 rg
277.286 574.170 37.879 0.750 re f
277.286 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 282.536 564.315 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
314.415 574.170 35.955 0.750 re f
314.415 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 319.665 564.315 Td /F1 9.8 Tf  [(1.5)] TJ ET
0.267 0.267 0.267 rg
349.620 574.170 40.771 0.750 re f
349.620 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 354.870 564.315 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
389.641 574.170 40.771 0.750 re f
389.641 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 394.891 564.315 Td /F1 9.8 Tf  [(1.2)] TJ ET
0.267 0.267 0.267 rg
429.662 574.170 39.815 0.750 re f
429.662 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 434.912 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
468.726 574.170 39.815 0.750 re f
468.726 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 473.976 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
507.791 574.170 37.879 0.750 re f
507.791 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 513.041 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
544.920 574.170 35.955 0.750 re f
544.920 550.657 0.750 24.263 re f
580.125 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 550.170 564.315 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
26.625 550.657 95.498 0.750 re f
26.625 534.776 95.498 0.750 re f
26.625 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 540.803 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
121.373 550.657 41.093 0.750 re f
121.373 534.776 41.093 0.750 re f
121.373 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 540.803 Td /F1 9.8 Tf  [(3.4)] TJ ET
0.267 0.267 0.267 rg
161.717 550.657 40.771 0.750 re f
161.717 534.776 40.771 0.750 re f
161.717 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 540.803 Td /F1 9.8 Tf  [(14.3)] TJ ET
0.267 0.267 0.267 rg
201.737 550.657 41.093 0.750 re f
201.737 534.776 41.093 0.750 re f
201.737 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 540.803 Td /F1 9.8 Tf  [(3.2)] TJ ET
0.267 0.267 0.267 rg
242.080 550.657 35.955 0.750 re f
242.080 534.776 35.955 0.750 re f
242.080 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 540.803 Td /F1 9.8 Tf  [(8.1)] TJ ET
0.267 0.267 0.267 rg
277.286 550.657 37.879 0.750 re f
277.286 534.776 37.879 0.750 re f
277.286 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 540.803 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
314.415 550.657 35.955 0.750 re f
314.415 534.776 35.955 0.750 re f
314.415 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 540.803 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
349.620 550.657 40.771 0.750 re f
349.620 534.776 40.771 0.750 re f
349.620 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 540.803 Td /F1 9.8 Tf  [(2.1)] TJ ET
0.267 0.267 0.267 rg
389.641 550.657 40.771 0.750 re f
389.641 534.776 40.771 0.750 re f
389.641 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 540.803 Td /F1 9.8 Tf  [(1.9)] TJ ET
0.267 0.267 0.267 rg
429.662 550.657 39.815 0.750 re f
429.662 534.776 39.815 0.750 re f
429.662 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 540.803 Td /F1 9.8 Tf  [(3.8)] TJ ET
0.267 0.267 0.267 rg
468.726 550.657 39.815 0.750 re f
468.726 534.776 39.815 0.750 re f
468.726 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 540.803 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
507.791 550.657 37.879 0.750 re f
507.791 534.776 37.879 0.750 re f
507.791 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 540.803 Td /F1 9.8 Tf  [(4.1)] TJ ET
0.267 0.267 0.267 rg
544.920 550.657 35.955 0.750 re f
544.920 534.776 35.955 0.750 re f
544.920 534.776 0.750 16.631 re f
580.125 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 540.803 Td /F1 9.8 Tf  [(0.4)] TJ ET
BT 26.250 487.377 Td /F4 9.8 Tf  [(Table 4: Comparison of missing branch rates and alignment SP-FN errors on the four largest datasets.)] TJ ET
BT 500.324 487.377 Td /F1 9.8 Tf  [( Each row lists )] TJ ET
BT 26.250 475.473 Td /F1 9.8 Tf  [(results for a method, and each column corresponds to a dataset. Missing branch rates \(%\) are with respect to the reference )] TJ ET
BT 26.250 463.568 Td /F1 9.8 Tf  [(tree. Alignment SP-FN errors \(%\) are with respect to the reference alignment. ML estimation was performed using RAxML on all )] TJ ET
BT 26.250 451.663 Td /F1 9.8 Tf  [(alignments with the exception of alignments estimated on the Price 78K dataset, for which we used FastTree \(we note this by )] TJ ET
BT 26.250 439.758 Td /F1 9.8 Tf  [(using the prefix �FT:� before the missing branch rate for the Price 78K dataset\). �F� indicates that the method aborted on the )] TJ ET
BT 26.250 427.854 Td /F1 9.8 Tf  [(dataset, and �s.r.� indicates that the method was still running on a 256 GB machine, at the time of submission of this manuscript. )] TJ ET
BT 26.250 415.949 Td /F1 9.8 Tf  [(Entry �n.a.� means �not attempted�; in the case of the results for ML trees produced on estimated alignments, this meant that )] TJ ET
BT 26.250 404.044 Td /F1 9.8 Tf  [(either we did not attempt to run the alignment, or that the alignment estimation did not complete. Entry �n.c.� for alignment SP-)] TJ ET
BT 26.250 392.139 Td /F1 9.8 Tf  [(FN error means �not computed�; this is given for those datasets that are so large that computing the alignment SP-FN error is )] TJ ET
BT 26.250 380.235 Td /F1 9.8 Tf  [(infeasible due to computational challenges. The Appendix provides further details about the hardware used for these )] TJ ET
BT 26.250 368.330 Td /F1 9.8 Tf  [(computations.)] TJ ET
1.000 1.000 1.000 rg
26.250 71.086 555.000 287.363 re f
0.267 0.267 0.267 rg
26.625 357.324 193.482 0.750 re f
26.625 341.443 0.750 16.631 re f
219.357 357.324 98.841 0.750 re f
318.198 357.324 116.090 0.750 re f
434.288 357.324 73.658 0.750 re f
507.946 357.324 72.929 0.750 re f
219.357 341.443 0.750 16.631 re f
580.125 341.443 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 347.469 Td /F4 9.8 Tf  [(Missing branch rate \(%\))] TJ ET
0.267 0.267 0.267 rg
26.625 341.443 193.482 0.750 re f
26.625 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 331.588 Td /F1 9.8 Tf  [(Method)] TJ ET
0.267 0.267 0.267 rg
219.357 341.443 99.216 0.750 re f
219.357 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 331.588 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
317.823 341.443 116.840 0.750 re f
317.823 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 331.588 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
433.913 341.443 74.408 0.750 re f
433.913 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 331.588 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
507.571 341.443 73.304 0.750 re f
507.571 325.562 0.750 16.631 re f
580.125 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 331.588 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
26.625 325.562 193.482 0.750 re f
26.625 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 315.707 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
219.357 325.562 99.216 0.750 re f
219.357 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 315.707 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 325.562 116.840 0.750 re f
317.823 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 315.707 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 325.562 74.408 0.750 re f
433.913 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 315.707 Td /F1 9.8 Tf  [(7.59)] TJ ET
0.267 0.267 0.267 rg
507.571 325.562 73.304 0.750 re f
507.571 309.680 0.750 16.631 re f
580.125 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 315.707 Td /F1 9.8 Tf  [(7.00)] TJ ET
0.267 0.267 0.267 rg
26.625 309.680 193.482 0.750 re f
26.625 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 299.825 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
219.357 309.680 99.216 0.750 re f
219.357 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 299.825 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 309.680 116.840 0.750 re f
317.823 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 299.825 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 309.680 74.408 0.750 re f
433.913 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 299.825 Td /F1 9.8 Tf  [(7.29)] TJ ET
0.267 0.267 0.267 rg
507.571 309.680 73.304 0.750 re f
507.571 293.799 0.750 16.631 re f
580.125 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 299.825 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 293.799 193.482 0.750 re f
26.625 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 283.944 Td /F1 9.8 Tf  [(ML\(MAFFT-PartTree\))] TJ ET
0.267 0.267 0.267 rg
219.357 293.799 99.216 0.750 re f
219.357 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 283.944 Td /F1 9.8 Tf  [(FT:9.14)] TJ ET
0.267 0.267 0.267 rg
317.823 293.799 116.840 0.750 re f
317.823 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 283.944 Td /F1 9.8 Tf  [(32.19)] TJ ET
0.267 0.267 0.267 rg
433.913 293.799 74.408 0.750 re f
433.913 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 283.944 Td /F1 9.8 Tf  [(16.73)] TJ ET
0.267 0.267 0.267 rg
507.571 293.799 73.304 0.750 re f
507.571 277.918 0.750 16.631 re f
580.125 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 283.944 Td /F1 9.8 Tf  [(11.83)] TJ ET
0.267 0.267 0.267 rg
26.625 277.918 193.482 0.750 re f
26.625 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 268.063 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
219.357 277.918 99.216 0.750 re f
219.357 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 268.063 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 277.918 116.840 0.750 re f
317.823 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 268.063 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 277.918 74.408 0.750 re f
433.913 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 268.063 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 277.918 73.304 0.750 re f
507.571 262.037 0.750 16.631 re f
580.125 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 268.063 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 262.037 193.482 0.750 re f
26.625 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 252.182 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
219.357 262.037 99.216 0.750 re f
219.357 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 252.182 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 262.037 116.840 0.750 re f
317.823 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
433.913 262.037 74.408 0.750 re f
433.913 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 262.037 73.304 0.750 re f
507.571 246.155 0.750 16.631 re f
580.125 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
26.625 246.155 193.482 0.750 re f
26.625 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 236.300 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
219.357 246.155 99.216 0.750 re f
219.357 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 236.300 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 246.155 116.840 0.750 re f
317.823 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 236.300 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 246.155 74.408 0.750 re f
433.913 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 236.300 Td /F1 9.8 Tf  [(10.21)] TJ ET
0.267 0.267 0.267 rg
507.571 246.155 73.304 0.750 re f
507.571 230.274 0.750 16.631 re f
580.125 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 236.300 Td /F1 9.8 Tf  [(9.29)] TJ ET
0.267 0.267 0.267 rg
26.625 230.274 193.482 0.750 re f
26.625 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 220.419 Td /F1 9.8 Tf  [(ML\(ClustalW-quicktree\))] TJ ET
0.267 0.267 0.267 rg
219.357 230.274 99.216 0.750 re f
219.357 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 220.419 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
317.823 230.274 116.840 0.750 re f
317.823 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 220.419 Td /F1 9.8 Tf  [(13.07)] TJ ET
0.267 0.267 0.267 rg
433.913 230.274 74.408 0.750 re f
433.913 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 220.419 Td /F1 9.8 Tf  [(34.23)] TJ ET
0.267 0.267 0.267 rg
507.571 230.274 73.304 0.750 re f
507.571 214.393 0.750 16.631 re f
580.125 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 220.419 Td /F1 9.8 Tf  [(31.47)] TJ ET
0.267 0.267 0.267 rg
26.625 214.393 193.482 0.750 re f
26.625 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 204.538 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
219.357 214.393 99.216 0.750 re f
219.357 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 204.538 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 214.393 116.840 0.750 re f
317.823 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 204.538 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 214.393 74.408 0.750 re f
433.913 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 204.538 Td /F1 9.8 Tf  [(18.62)] TJ ET
0.267 0.267 0.267 rg
507.571 214.393 73.304 0.750 re f
507.571 198.511 0.750 16.631 re f
580.125 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 204.538 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 198.511 193.482 0.750 re f
26.625 182.630 0.750 16.631 re f
219.357 198.511 98.841 0.750 re f
318.198 198.511 116.090 0.750 re f
434.288 198.511 73.658 0.750 re f
507.946 198.511 72.929 0.750 re f
219.357 182.630 0.750 16.631 re f
580.125 182.630 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 188.656 Td /F4 9.8 Tf  [(Alignment SP-FN error \(%\))] TJ ET
0.267 0.267 0.267 rg
26.625 182.630 193.482 0.750 re f
26.625 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 172.775 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
219.357 182.630 99.216 0.750 re f
219.357 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 172.775 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
317.823 182.630 116.840 0.750 re f
317.823 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 172.775 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
433.913 182.630 74.408 0.750 re f
433.913 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 172.775 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
507.571 182.630 73.304 0.750 re f
507.571 166.749 0.750 16.631 re f
580.125 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 172.775 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
26.625 166.749 193.482 0.750 re f
26.625 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 156.894 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
219.357 166.749 99.216 0.750 re f
219.357 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 156.894 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 166.749 116.840 0.750 re f
317.823 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 156.894 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 166.749 74.408 0.750 re f
433.913 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 156.894 Td /F1 9.8 Tf  [(36.96)] TJ ET
0.267 0.267 0.267 rg
507.571 166.749 73.304 0.750 re f
507.571 150.868 0.750 16.631 re f
580.125 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 156.894 Td /F1 9.8 Tf  [(24.93)] TJ ET
0.267 0.267 0.267 rg
26.625 150.868 193.482 0.750 re f
26.625 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 141.013 Td /F1 9.8 Tf  [(MAFFT)] TJ ET
0.267 0.267 0.267 rg
219.357 150.868 99.216 0.750 re f
219.357 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 141.013 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 150.868 116.840 0.750 re f
317.823 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 141.013 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 150.868 74.408 0.750 re f
433.913 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 141.013 Td /F1 9.8 Tf  [(30.97)] TJ ET
0.267 0.267 0.267 rg
507.571 150.868 73.304 0.750 re f
507.571 134.986 0.750 16.631 re f
580.125 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 141.013 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 134.986 193.482 0.750 re f
26.625 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 125.131 Td /F1 9.8 Tf  [(MAFFT-PartTree)] TJ ET
0.267 0.267 0.267 rg
219.357 134.986 99.216 0.750 re f
219.357 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 125.131 Td /F1 9.8 Tf  [(n.c.)] TJ ET
0.267 0.267 0.267 rg
317.823 134.986 116.840 0.750 re f
317.823 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 125.131 Td /F1 9.8 Tf  [(41.73)] TJ ET
0.267 0.267 0.267 rg
433.913 134.986 74.408 0.750 re f
433.913 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 125.131 Td /F1 9.8 Tf  [(34.29)] TJ ET
0.267 0.267 0.267 rg
507.571 134.986 73.304 0.750 re f
507.571 119.105 0.750 16.631 re f
580.125 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 125.131 Td /F1 9.8 Tf  [(22.64)] TJ ET
0.267 0.267 0.267 rg
26.625 119.105 193.482 0.750 re f
26.625 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 109.250 Td /F1 9.8 Tf  [(Prank+GT)] TJ ET
0.267 0.267 0.267 rg
219.357 119.105 99.216 0.750 re f
219.357 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 109.250 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 119.105 116.840 0.750 re f
317.823 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 109.250 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 119.105 74.408 0.750 re f
433.913 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 109.250 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 119.105 73.304 0.750 re f
507.571 103.224 0.750 16.631 re f
580.125 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 109.250 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 103.224 193.482 0.750 re f
26.625 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 93.369 Td /F1 9.8 Tf  [(Muscle)] TJ ET
0.267 0.267 0.267 rg
219.357 103.224 99.216 0.750 re f
219.357 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 93.369 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 103.224 116.840 0.750 re f
317.823 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
433.913 103.224 74.408 0.750 re f
433.913 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 103.224 73.304 0.750 re f
507.571 87.343 0.750 16.631 re f
580.125 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
26.625 87.343 193.482 0.750 re f
26.625 71.461 193.482 0.750 re f
26.625 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 77.488 Td /F1 9.8 Tf  [(ClustalW)] TJ ET
0.267 0.267 0.267 rg
219.357 87.343 99.216 0.750 re f
219.357 71.461 99.216 0.750 re f
219.357 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 77.488 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 87.343 116.840 0.750 re f
317.823 71.461 116.840 0.750 re f
317.823 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 77.488 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 87.343 74.408 0.750 re f
433.913 71.461 74.408 0.750 re f
433.913 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 77.488 Td /F1 9.8 Tf  [(56.33)] TJ ET
0.267 0.267 0.267 rg
507.571 87.343 73.304 0.750 re f
507.571 71.461 73.304 0.750 re f
507.571 71.461 0.750 16.631 re f
580.125 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 77.488 Td /F1 9.8 Tf  [(52.04)] TJ ET
Q
q
15.000 71.086 577.500 705.914 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(column corresponds to a dataset. All analyses succeeded using a dedicated computing core with dedicated access to at least )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(512 MB and at most 4 GB of main memory. The Appendix provides further details about the hardware used for these )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(computations. ML tree estimation was performed using RAxML. The runtimes given for SAT� include the initial phase, which )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(includes the calculation of the four two-phase methods, followed by a 24 hour analysis. We do not divide SAT�s runtime into )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(time used for alignment and tree estimation, but just show the total.)] TJ ET
1.000 1.000 1.000 rg
26.250 534.401 555.000 175.575 re f
0.267 0.267 0.267 rg
26.625 708.851 95.498 0.750 re f
26.625 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 698.996 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
121.373 708.851 40.718 0.750 re f
162.092 708.851 40.396 0.750 re f
121.373 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 698.996 Td /F1 9.8 Tf  [(16S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
201.737 708.851 40.718 0.750 re f
242.455 708.851 35.580 0.750 re f
201.737 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 698.996 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
277.286 708.851 37.504 0.750 re f
314.790 708.851 35.580 0.750 re f
277.286 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 698.996 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
349.620 708.851 40.396 0.750 re f
390.016 708.851 40.396 0.750 re f
349.620 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 698.996 Td /F1 9.8 Tf  [(23S.M.aa_ag)] TJ ET
0.267 0.267 0.267 rg
429.662 708.851 39.440 0.750 re f
469.101 708.851 39.440 0.750 re f
429.662 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 698.996 Td /F1 9.8 Tf  [(23S.E.aa_ag)] TJ ET
0.267 0.267 0.267 rg
507.791 708.851 37.504 0.750 re f
545.295 708.851 35.580 0.750 re f
507.791 692.970 0.750 16.631 re f
580.125 692.970 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 698.996 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
26.625 692.970 95.498 0.750 re f
26.625 677.089 0.750 16.631 re f
121.373 692.970 41.093 0.750 re f
121.373 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
161.717 692.970 40.771 0.750 re f
161.717 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
201.737 692.970 41.093 0.750 re f
201.737 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
242.080 692.970 35.955 0.750 re f
242.080 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
277.286 692.970 37.879 0.750 re f
277.286 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
314.415 692.970 35.955 0.750 re f
314.415 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
349.620 692.970 40.771 0.750 re f
349.620 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
389.641 692.970 40.771 0.750 re f
389.641 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
429.662 692.970 39.815 0.750 re f
429.662 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
468.726 692.970 39.815 0.750 re f
468.726 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
507.791 692.970 37.879 0.750 re f
507.791 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 683.115 Td /F1 9.8 Tf  [(Align)] TJ ET
0.267 0.267 0.267 rg
544.920 692.970 35.955 0.750 re f
544.920 677.089 0.750 16.631 re f
580.125 677.089 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 683.115 Td /F1 9.8 Tf  [(Tree)] TJ ET
0.267 0.267 0.267 rg
26.625 677.089 95.498 0.750 re f
26.625 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 667.234 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
121.373 677.089 41.093 0.750 re f
121.373 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 667.234 Td /F1 9.8 Tf  [(114.5)] TJ ET
0.267 0.267 0.267 rg
161.717 677.089 40.771 0.750 re f
161.717 661.207 0.750 16.631 re f
201.737 677.089 41.093 0.750 re f
201.737 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 667.234 Td /F1 9.8 Tf  [(106.0)] TJ ET
0.267 0.267 0.267 rg
242.080 677.089 35.955 0.750 re f
242.080 661.207 0.750 16.631 re f
277.286 677.089 37.879 0.750 re f
277.286 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 667.234 Td /F1 9.8 Tf  [(68.9)] TJ ET
0.267 0.267 0.267 rg
314.415 677.089 35.955 0.750 re f
314.415 661.207 0.750 16.631 re f
349.620 677.089 40.771 0.750 re f
349.620 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 667.234 Td /F1 9.8 Tf  [(67.2)] TJ ET
0.267 0.267 0.267 rg
389.641 677.089 40.771 0.750 re f
389.641 661.207 0.750 16.631 re f
429.662 677.089 39.815 0.750 re f
429.662 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 667.234 Td /F1 9.8 Tf  [(61.8)] TJ ET
0.267 0.267 0.267 rg
468.726 677.089 39.815 0.750 re f
468.726 661.207 0.750 16.631 re f
507.791 677.089 37.879 0.750 re f
507.791 661.207 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 667.234 Td /F1 9.8 Tf  [(60.0)] TJ ET
0.267 0.267 0.267 rg
544.920 677.089 35.955 0.750 re f
544.920 661.207 0.750 16.631 re f
580.125 661.207 0.750 16.631 re f
26.625 661.207 95.498 0.750 re f
26.625 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 651.353 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
121.373 661.207 41.093 0.750 re f
121.373 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 651.353 Td /F1 9.8 Tf  [(9.2)] TJ ET
0.267 0.267 0.267 rg
161.717 661.207 40.771 0.750 re f
161.717 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 651.353 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
201.737 661.207 41.093 0.750 re f
201.737 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 651.353 Td /F1 9.8 Tf  [(5.8)] TJ ET
0.267 0.267 0.267 rg
242.080 661.207 35.955 0.750 re f
242.080 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 651.353 Td /F1 9.8 Tf  [(3.6)] TJ ET
0.267 0.267 0.267 rg
277.286 661.207 37.879 0.750 re f
277.286 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 651.353 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
314.415 661.207 35.955 0.750 re f
314.415 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 651.353 Td /F1 9.8 Tf  [(2.2)] TJ ET
0.267 0.267 0.267 rg
349.620 661.207 40.771 0.750 re f
349.620 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 651.353 Td /F1 9.8 Tf  [(1.7)] TJ ET
0.267 0.267 0.267 rg
389.641 661.207 40.771 0.750 re f
389.641 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 651.353 Td /F1 9.8 Tf  [(1.1)] TJ ET
0.267 0.267 0.267 rg
429.662 661.207 39.815 0.750 re f
429.662 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 651.353 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
468.726 661.207 39.815 0.750 re f
468.726 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 651.353 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
507.791 661.207 37.879 0.750 re f
507.791 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 651.353 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
544.920 661.207 35.955 0.750 re f
544.920 645.326 0.750 16.631 re f
580.125 645.326 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 651.353 Td /F1 9.8 Tf  [(0.3)] TJ ET
0.267 0.267 0.267 rg
26.625 645.326 95.498 0.750 re f
26.625 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 635.471 Td /F1 9.8 Tf  [(ML\(MAFFT-)] TJ ET
BT 31.875 627.840 Td /F1 9.8 Tf  [(PartTree\))] TJ ET
0.267 0.267 0.267 rg
121.373 645.326 41.093 0.750 re f
121.373 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 126.623 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
161.717 645.326 40.771 0.750 re f
161.717 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 166.967 635.471 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
201.737 645.326 41.093 0.750 re f
201.737 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 206.987 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
242.080 645.326 35.955 0.750 re f
242.080 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 247.330 635.471 Td /F1 9.8 Tf  [(6.6)] TJ ET
0.267 0.267 0.267 rg
277.286 645.326 37.879 0.750 re f
277.286 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 282.536 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
314.415 645.326 35.955 0.750 re f
314.415 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 319.665 635.471 Td /F1 9.8 Tf  [(1.9)] TJ ET
0.267 0.267 0.267 rg
349.620 645.326 40.771 0.750 re f
349.620 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 354.870 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
389.641 645.326 40.771 0.750 re f
389.641 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 394.891 635.471 Td /F1 9.8 Tf  [(1.6)] TJ ET
0.267 0.267 0.267 rg
429.662 645.326 39.815 0.750 re f
429.662 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 434.912 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
468.726 645.326 39.815 0.750 re f
468.726 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 473.976 635.471 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
507.791 645.326 37.879 0.750 re f
507.791 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 513.041 635.471 Td /F1 9.8 Tf  [(<0.1)] TJ ET
0.267 0.267 0.267 rg
544.920 645.326 35.955 0.750 re f
544.920 621.814 0.750 24.263 re f
580.125 621.814 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 550.170 635.471 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
26.625 621.814 95.498 0.750 re f
26.625 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 611.959 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
121.373 621.814 41.093 0.750 re f
121.373 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 611.959 Td /F1 9.8 Tf  [(15.4)] TJ ET
0.267 0.267 0.267 rg
161.717 621.814 40.771 0.750 re f
161.717 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 611.959 Td /F1 9.8 Tf  [(17.1)] TJ ET
0.267 0.267 0.267 rg
201.737 621.814 41.093 0.750 re f
201.737 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 611.959 Td /F1 9.8 Tf  [(9.7)] TJ ET
0.267 0.267 0.267 rg
242.080 621.814 35.955 0.750 re f
242.080 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 611.959 Td /F1 9.8 Tf  [(12.5)] TJ ET
0.267 0.267 0.267 rg
277.286 621.814 37.879 0.750 re f
277.286 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 611.959 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
314.415 621.814 35.955 0.750 re f
314.415 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 611.959 Td /F1 9.8 Tf  [(3.3)] TJ ET
0.267 0.267 0.267 rg
349.620 621.814 40.771 0.750 re f
349.620 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 611.959 Td /F1 9.8 Tf  [(5.3)] TJ ET
0.267 0.267 0.267 rg
389.641 621.814 40.771 0.750 re f
389.641 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 611.959 Td /F1 9.8 Tf  [(2.6)] TJ ET
0.267 0.267 0.267 rg
429.662 621.814 39.815 0.750 re f
429.662 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 611.959 Td /F1 9.8 Tf  [(8.3)] TJ ET
0.267 0.267 0.267 rg
468.726 621.814 39.815 0.750 re f
468.726 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 611.959 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
507.791 621.814 37.879 0.750 re f
507.791 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 611.959 Td /F1 9.8 Tf  [(7.4)] TJ ET
0.267 0.267 0.267 rg
544.920 621.814 35.955 0.750 re f
544.920 605.933 0.750 16.631 re f
580.125 605.933 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 611.959 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
26.625 605.933 95.498 0.750 re f
26.625 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 596.077 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
121.373 605.933 41.093 0.750 re f
121.373 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 596.077 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
161.717 605.933 40.771 0.750 re f
161.717 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 596.077 Td /F1 9.8 Tf  [(6.1)] TJ ET
0.267 0.267 0.267 rg
201.737 605.933 41.093 0.750 re f
201.737 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 596.077 Td /F1 9.8 Tf  [(10.3)] TJ ET
0.267 0.267 0.267 rg
242.080 605.933 35.955 0.750 re f
242.080 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 596.077 Td /F1 9.8 Tf  [(7.6)] TJ ET
0.267 0.267 0.267 rg
277.286 605.933 37.879 0.750 re f
277.286 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 596.077 Td /F1 9.8 Tf  [(3.1)] TJ ET
0.267 0.267 0.267 rg
314.415 605.933 35.955 0.750 re f
314.415 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 596.077 Td /F1 9.8 Tf  [(1.1)] TJ ET
0.267 0.267 0.267 rg
349.620 605.933 40.771 0.750 re f
349.620 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 596.077 Td /F1 9.8 Tf  [(2.5)] TJ ET
0.267 0.267 0.267 rg
389.641 605.933 40.771 0.750 re f
389.641 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 596.077 Td /F1 9.8 Tf  [(1.6)] TJ ET
0.267 0.267 0.267 rg
429.662 605.933 39.815 0.750 re f
429.662 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 596.077 Td /F1 9.8 Tf  [(0.6)] TJ ET
0.267 0.267 0.267 rg
468.726 605.933 39.815 0.750 re f
468.726 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 596.077 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
507.791 605.933 37.879 0.750 re f
507.791 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 596.077 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
544.920 605.933 35.955 0.750 re f
544.920 590.051 0.750 16.631 re f
580.125 590.051 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 596.077 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
26.625 590.051 95.498 0.750 re f
26.625 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 580.196 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
121.373 590.051 41.093 0.750 re f
121.373 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 580.196 Td /F1 9.8 Tf  [(5.6)] TJ ET
0.267 0.267 0.267 rg
161.717 590.051 40.771 0.750 re f
161.717 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 580.196 Td /F1 9.8 Tf  [(4.5)] TJ ET
0.267 0.267 0.267 rg
201.737 590.051 41.093 0.750 re f
201.737 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 580.196 Td /F1 9.8 Tf  [(6.3)] TJ ET
0.267 0.267 0.267 rg
242.080 590.051 35.955 0.750 re f
242.080 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 580.196 Td /F1 9.8 Tf  [(2.5)] TJ ET
0.267 0.267 0.267 rg
277.286 590.051 37.879 0.750 re f
277.286 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 580.196 Td /F1 9.8 Tf  [(1.5)] TJ ET
0.267 0.267 0.267 rg
314.415 590.051 35.955 0.750 re f
314.415 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 580.196 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
349.620 590.051 40.771 0.750 re f
349.620 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 580.196 Td /F1 9.8 Tf  [(1.3)] TJ ET
0.267 0.267 0.267 rg
389.641 590.051 40.771 0.750 re f
389.641 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 580.196 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
429.662 590.051 39.815 0.750 re f
429.662 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 580.196 Td /F1 9.8 Tf  [(2.0)] TJ ET
0.267 0.267 0.267 rg
468.726 590.051 39.815 0.750 re f
468.726 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 580.196 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
507.791 590.051 37.879 0.750 re f
507.791 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 580.196 Td /F1 9.8 Tf  [(1.7)] TJ ET
0.267 0.267 0.267 rg
544.920 590.051 35.955 0.750 re f
544.920 574.170 0.750 16.631 re f
580.125 574.170 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 580.196 Td /F1 9.8 Tf  [(0.3)] TJ ET
0.267 0.267 0.267 rg
26.625 574.170 95.498 0.750 re f
26.625 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 31.875 564.315 Td /F1 9.8 Tf  [(ML\(ClustalW-)] TJ ET
BT 31.875 556.684 Td /F1 9.8 Tf  [(quicktree\))] TJ ET
0.267 0.267 0.267 rg
121.373 574.170 41.093 0.750 re f
121.373 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 126.623 564.315 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
161.717 574.170 40.771 0.750 re f
161.717 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 166.967 564.315 Td /F1 9.8 Tf  [(4.3)] TJ ET
0.267 0.267 0.267 rg
201.737 574.170 41.093 0.750 re f
201.737 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 206.987 564.315 Td /F1 9.8 Tf  [(0.9)] TJ ET
0.267 0.267 0.267 rg
242.080 574.170 35.955 0.750 re f
242.080 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 247.330 564.315 Td /F1 9.8 Tf  [(3.6)] TJ ET
0.267 0.267 0.267 rg
277.286 574.170 37.879 0.750 re f
277.286 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 282.536 564.315 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
314.415 574.170 35.955 0.750 re f
314.415 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 319.665 564.315 Td /F1 9.8 Tf  [(1.5)] TJ ET
0.267 0.267 0.267 rg
349.620 574.170 40.771 0.750 re f
349.620 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 354.870 564.315 Td /F1 9.8 Tf  [(0.4)] TJ ET
0.267 0.267 0.267 rg
389.641 574.170 40.771 0.750 re f
389.641 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 394.891 564.315 Td /F1 9.8 Tf  [(1.2)] TJ ET
0.267 0.267 0.267 rg
429.662 574.170 39.815 0.750 re f
429.662 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 434.912 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
468.726 574.170 39.815 0.750 re f
468.726 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 473.976 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
507.791 574.170 37.879 0.750 re f
507.791 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 513.041 564.315 Td /F1 9.8 Tf  [(0.7)] TJ ET
0.267 0.267 0.267 rg
544.920 574.170 35.955 0.750 re f
544.920 550.657 0.750 24.263 re f
580.125 550.657 0.750 24.263 re f
0.271 0.267 0.267 rg
BT 550.170 564.315 Td /F1 9.8 Tf  [(0.5)] TJ ET
0.267 0.267 0.267 rg
26.625 550.657 95.498 0.750 re f
26.625 534.776 95.498 0.750 re f
26.625 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 540.803 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
121.373 550.657 41.093 0.750 re f
121.373 534.776 41.093 0.750 re f
121.373 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 126.623 540.803 Td /F1 9.8 Tf  [(3.4)] TJ ET
0.267 0.267 0.267 rg
161.717 550.657 40.771 0.750 re f
161.717 534.776 40.771 0.750 re f
161.717 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 166.967 540.803 Td /F1 9.8 Tf  [(14.3)] TJ ET
0.267 0.267 0.267 rg
201.737 550.657 41.093 0.750 re f
201.737 534.776 41.093 0.750 re f
201.737 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 206.987 540.803 Td /F1 9.8 Tf  [(3.2)] TJ ET
0.267 0.267 0.267 rg
242.080 550.657 35.955 0.750 re f
242.080 534.776 35.955 0.750 re f
242.080 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 247.330 540.803 Td /F1 9.8 Tf  [(8.1)] TJ ET
0.267 0.267 0.267 rg
277.286 550.657 37.879 0.750 re f
277.286 534.776 37.879 0.750 re f
277.286 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 282.536 540.803 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
314.415 550.657 35.955 0.750 re f
314.415 534.776 35.955 0.750 re f
314.415 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 319.665 540.803 Td /F1 9.8 Tf  [(2.8)] TJ ET
0.267 0.267 0.267 rg
349.620 550.657 40.771 0.750 re f
349.620 534.776 40.771 0.750 re f
349.620 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 354.870 540.803 Td /F1 9.8 Tf  [(2.1)] TJ ET
0.267 0.267 0.267 rg
389.641 550.657 40.771 0.750 re f
389.641 534.776 40.771 0.750 re f
389.641 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 394.891 540.803 Td /F1 9.8 Tf  [(1.9)] TJ ET
0.267 0.267 0.267 rg
429.662 550.657 39.815 0.750 re f
429.662 534.776 39.815 0.750 re f
429.662 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 434.912 540.803 Td /F1 9.8 Tf  [(3.8)] TJ ET
0.267 0.267 0.267 rg
468.726 550.657 39.815 0.750 re f
468.726 534.776 39.815 0.750 re f
468.726 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 473.976 540.803 Td /F1 9.8 Tf  [(0.8)] TJ ET
0.267 0.267 0.267 rg
507.791 550.657 37.879 0.750 re f
507.791 534.776 37.879 0.750 re f
507.791 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 513.041 540.803 Td /F1 9.8 Tf  [(4.1)] TJ ET
0.267 0.267 0.267 rg
544.920 550.657 35.955 0.750 re f
544.920 534.776 35.955 0.750 re f
544.920 534.776 0.750 16.631 re f
580.125 534.776 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 550.170 540.803 Td /F1 9.8 Tf  [(0.4)] TJ ET
BT 26.250 487.377 Td /F4 9.8 Tf  [(Table 4: Comparison of missing branch rates and alignment SP-FN errors on the four largest datasets.)] TJ ET
BT 500.324 487.377 Td /F1 9.8 Tf  [( Each row lists )] TJ ET
BT 26.250 475.473 Td /F1 9.8 Tf  [(results for a method, and each column corresponds to a dataset. Missing branch rates \(%\) are with respect to the reference )] TJ ET
BT 26.250 463.568 Td /F1 9.8 Tf  [(tree. Alignment SP-FN errors \(%\) are with respect to the reference alignment. ML estimation was performed using RAxML on all )] TJ ET
BT 26.250 451.663 Td /F1 9.8 Tf  [(alignments with the exception of alignments estimated on the Price 78K dataset, for which we used FastTree \(we note this by )] TJ ET
BT 26.250 439.758 Td /F1 9.8 Tf  [(using the prefix �FT:� before the missing branch rate for the Price 78K dataset\). �F� indicates that the method aborted on the )] TJ ET
BT 26.250 427.854 Td /F1 9.8 Tf  [(dataset, and �s.r.� indicates that the method was still running on a 256 GB machine, at the time of submission of this manuscript. )] TJ ET
BT 26.250 415.949 Td /F1 9.8 Tf  [(Entry �n.a.� means �not attempted�; in the case of the results for ML trees produced on estimated alignments, this meant that )] TJ ET
BT 26.250 404.044 Td /F1 9.8 Tf  [(either we did not attempt to run the alignment, or that the alignment estimation did not complete. Entry �n.c.� for alignment SP-)] TJ ET
BT 26.250 392.139 Td /F1 9.8 Tf  [(FN error means �not computed�; this is given for those datasets that are so large that computing the alignment SP-FN error is )] TJ ET
BT 26.250 380.235 Td /F1 9.8 Tf  [(infeasible due to computational challenges. The Appendix provides further details about the hardware used for these )] TJ ET
BT 26.250 368.330 Td /F1 9.8 Tf  [(computations.)] TJ ET
1.000 1.000 1.000 rg
26.250 71.086 555.000 287.363 re f
0.267 0.267 0.267 rg
26.625 357.324 193.482 0.750 re f
26.625 341.443 0.750 16.631 re f
219.357 357.324 98.841 0.750 re f
318.198 357.324 116.090 0.750 re f
434.288 357.324 73.658 0.750 re f
507.946 357.324 72.929 0.750 re f
219.357 341.443 0.750 16.631 re f
580.125 341.443 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 347.469 Td /F4 9.8 Tf  [(Missing branch rate \(%\))] TJ ET
0.267 0.267 0.267 rg
26.625 341.443 193.482 0.750 re f
26.625 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 331.588 Td /F1 9.8 Tf  [(Method)] TJ ET
0.267 0.267 0.267 rg
219.357 341.443 99.216 0.750 re f
219.357 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 331.588 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
317.823 341.443 116.840 0.750 re f
317.823 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 331.588 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
433.913 341.443 74.408 0.750 re f
433.913 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 331.588 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
507.571 341.443 73.304 0.750 re f
507.571 325.562 0.750 16.631 re f
580.125 325.562 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 331.588 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
26.625 325.562 193.482 0.750 re f
26.625 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 315.707 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
219.357 325.562 99.216 0.750 re f
219.357 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 315.707 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 325.562 116.840 0.750 re f
317.823 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 315.707 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 325.562 74.408 0.750 re f
433.913 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 315.707 Td /F1 9.8 Tf  [(7.59)] TJ ET
0.267 0.267 0.267 rg
507.571 325.562 73.304 0.750 re f
507.571 309.680 0.750 16.631 re f
580.125 309.680 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 315.707 Td /F1 9.8 Tf  [(7.00)] TJ ET
0.267 0.267 0.267 rg
26.625 309.680 193.482 0.750 re f
26.625 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 299.825 Td /F1 9.8 Tf  [(ML\(MAFFT\))] TJ ET
0.267 0.267 0.267 rg
219.357 309.680 99.216 0.750 re f
219.357 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 299.825 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 309.680 116.840 0.750 re f
317.823 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 299.825 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 309.680 74.408 0.750 re f
433.913 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 299.825 Td /F1 9.8 Tf  [(7.29)] TJ ET
0.267 0.267 0.267 rg
507.571 309.680 73.304 0.750 re f
507.571 293.799 0.750 16.631 re f
580.125 293.799 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 299.825 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 293.799 193.482 0.750 re f
26.625 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 283.944 Td /F1 9.8 Tf  [(ML\(MAFFT-PartTree\))] TJ ET
0.267 0.267 0.267 rg
219.357 293.799 99.216 0.750 re f
219.357 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 283.944 Td /F1 9.8 Tf  [(FT:9.14)] TJ ET
0.267 0.267 0.267 rg
317.823 293.799 116.840 0.750 re f
317.823 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 283.944 Td /F1 9.8 Tf  [(32.19)] TJ ET
0.267 0.267 0.267 rg
433.913 293.799 74.408 0.750 re f
433.913 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 283.944 Td /F1 9.8 Tf  [(16.73)] TJ ET
0.267 0.267 0.267 rg
507.571 293.799 73.304 0.750 re f
507.571 277.918 0.750 16.631 re f
580.125 277.918 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 283.944 Td /F1 9.8 Tf  [(11.83)] TJ ET
0.267 0.267 0.267 rg
26.625 277.918 193.482 0.750 re f
26.625 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 268.063 Td /F1 9.8 Tf  [(ML\(Prank+GT\))] TJ ET
0.267 0.267 0.267 rg
219.357 277.918 99.216 0.750 re f
219.357 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 268.063 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 277.918 116.840 0.750 re f
317.823 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 268.063 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 277.918 74.408 0.750 re f
433.913 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 268.063 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 277.918 73.304 0.750 re f
507.571 262.037 0.750 16.631 re f
580.125 262.037 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 268.063 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 262.037 193.482 0.750 re f
26.625 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 252.182 Td /F1 9.8 Tf  [(ML\(Muscle\))] TJ ET
0.267 0.267 0.267 rg
219.357 262.037 99.216 0.750 re f
219.357 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 252.182 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 262.037 116.840 0.750 re f
317.823 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
433.913 262.037 74.408 0.750 re f
433.913 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 262.037 73.304 0.750 re f
507.571 246.155 0.750 16.631 re f
580.125 246.155 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 252.182 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
26.625 246.155 193.482 0.750 re f
26.625 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 236.300 Td /F1 9.8 Tf  [(ML\(ClustalW\))] TJ ET
0.267 0.267 0.267 rg
219.357 246.155 99.216 0.750 re f
219.357 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 236.300 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 246.155 116.840 0.750 re f
317.823 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 236.300 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 246.155 74.408 0.750 re f
433.913 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 236.300 Td /F1 9.8 Tf  [(10.21)] TJ ET
0.267 0.267 0.267 rg
507.571 246.155 73.304 0.750 re f
507.571 230.274 0.750 16.631 re f
580.125 230.274 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 236.300 Td /F1 9.8 Tf  [(9.29)] TJ ET
0.267 0.267 0.267 rg
26.625 230.274 193.482 0.750 re f
26.625 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 220.419 Td /F1 9.8 Tf  [(ML\(ClustalW-quicktree\))] TJ ET
0.267 0.267 0.267 rg
219.357 230.274 99.216 0.750 re f
219.357 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 220.419 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
317.823 230.274 116.840 0.750 re f
317.823 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 220.419 Td /F1 9.8 Tf  [(13.07)] TJ ET
0.267 0.267 0.267 rg
433.913 230.274 74.408 0.750 re f
433.913 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 220.419 Td /F1 9.8 Tf  [(34.23)] TJ ET
0.267 0.267 0.267 rg
507.571 230.274 73.304 0.750 re f
507.571 214.393 0.750 16.631 re f
580.125 214.393 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 220.419 Td /F1 9.8 Tf  [(31.47)] TJ ET
0.267 0.267 0.267 rg
26.625 214.393 193.482 0.750 re f
26.625 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 204.538 Td /F1 9.8 Tf  [(ML\(Opal\))] TJ ET
0.267 0.267 0.267 rg
219.357 214.393 99.216 0.750 re f
219.357 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 204.538 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 214.393 116.840 0.750 re f
317.823 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 204.538 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 214.393 74.408 0.750 re f
433.913 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 204.538 Td /F1 9.8 Tf  [(18.62)] TJ ET
0.267 0.267 0.267 rg
507.571 214.393 73.304 0.750 re f
507.571 198.511 0.750 16.631 re f
580.125 198.511 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 204.538 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 198.511 193.482 0.750 re f
26.625 182.630 0.750 16.631 re f
219.357 198.511 98.841 0.750 re f
318.198 198.511 116.090 0.750 re f
434.288 198.511 73.658 0.750 re f
507.946 198.511 72.929 0.750 re f
219.357 182.630 0.750 16.631 re f
580.125 182.630 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 188.656 Td /F4 9.8 Tf  [(Alignment SP-FN error \(%\))] TJ ET
0.267 0.267 0.267 rg
26.625 182.630 193.482 0.750 re f
26.625 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 172.775 Td /F1 9.8 Tf  [(Dataset)] TJ ET
0.267 0.267 0.267 rg
219.357 182.630 99.216 0.750 re f
219.357 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 172.775 Td /F1 9.8 Tf  [(Price 78K)] TJ ET
0.267 0.267 0.267 rg
317.823 182.630 116.840 0.750 re f
317.823 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 172.775 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.267 0.267 0.267 rg
433.913 182.630 74.408 0.750 re f
433.913 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 172.775 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
507.571 182.630 73.304 0.750 re f
507.571 166.749 0.750 16.631 re f
580.125 166.749 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 172.775 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
26.625 166.749 193.482 0.750 re f
26.625 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 156.894 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
219.357 166.749 99.216 0.750 re f
219.357 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 156.894 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 166.749 116.840 0.750 re f
317.823 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 156.894 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 166.749 74.408 0.750 re f
433.913 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 156.894 Td /F1 9.8 Tf  [(36.96)] TJ ET
0.267 0.267 0.267 rg
507.571 166.749 73.304 0.750 re f
507.571 150.868 0.750 16.631 re f
580.125 150.868 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 156.894 Td /F1 9.8 Tf  [(24.93)] TJ ET
0.267 0.267 0.267 rg
26.625 150.868 193.482 0.750 re f
26.625 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 141.013 Td /F1 9.8 Tf  [(MAFFT)] TJ ET
0.267 0.267 0.267 rg
219.357 150.868 99.216 0.750 re f
219.357 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 141.013 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 150.868 116.840 0.750 re f
317.823 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 141.013 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 150.868 74.408 0.750 re f
433.913 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 141.013 Td /F1 9.8 Tf  [(30.97)] TJ ET
0.267 0.267 0.267 rg
507.571 150.868 73.304 0.750 re f
507.571 134.986 0.750 16.631 re f
580.125 134.986 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 141.013 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 134.986 193.482 0.750 re f
26.625 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 125.131 Td /F1 9.8 Tf  [(MAFFT-PartTree)] TJ ET
0.267 0.267 0.267 rg
219.357 134.986 99.216 0.750 re f
219.357 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 125.131 Td /F1 9.8 Tf  [(n.c.)] TJ ET
0.267 0.267 0.267 rg
317.823 134.986 116.840 0.750 re f
317.823 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 125.131 Td /F1 9.8 Tf  [(41.73)] TJ ET
0.267 0.267 0.267 rg
433.913 134.986 74.408 0.750 re f
433.913 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 125.131 Td /F1 9.8 Tf  [(34.29)] TJ ET
0.267 0.267 0.267 rg
507.571 134.986 73.304 0.750 re f
507.571 119.105 0.750 16.631 re f
580.125 119.105 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 125.131 Td /F1 9.8 Tf  [(22.64)] TJ ET
0.267 0.267 0.267 rg
26.625 119.105 193.482 0.750 re f
26.625 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 109.250 Td /F1 9.8 Tf  [(Prank+GT)] TJ ET
0.267 0.267 0.267 rg
219.357 119.105 99.216 0.750 re f
219.357 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 109.250 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 119.105 116.840 0.750 re f
317.823 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 109.250 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 119.105 74.408 0.750 re f
433.913 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 109.250 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 119.105 73.304 0.750 re f
507.571 103.224 0.750 16.631 re f
580.125 103.224 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 109.250 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
26.625 103.224 193.482 0.750 re f
26.625 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 93.369 Td /F1 9.8 Tf  [(Muscle)] TJ ET
0.267 0.267 0.267 rg
219.357 103.224 99.216 0.750 re f
219.357 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 93.369 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 103.224 116.840 0.750 re f
317.823 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
433.913 103.224 74.408 0.750 re f
433.913 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
507.571 103.224 73.304 0.750 re f
507.571 87.343 0.750 16.631 re f
580.125 87.343 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 93.369 Td /F1 9.8 Tf  [(s.r.)] TJ ET
0.267 0.267 0.267 rg
26.625 87.343 193.482 0.750 re f
26.625 71.461 193.482 0.750 re f
26.625 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 77.488 Td /F1 9.8 Tf  [(ClustalW)] TJ ET
0.267 0.267 0.267 rg
219.357 87.343 99.216 0.750 re f
219.357 71.461 99.216 0.750 re f
219.357 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 77.488 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 87.343 116.840 0.750 re f
317.823 71.461 116.840 0.750 re f
317.823 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 77.488 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 87.343 74.408 0.750 re f
433.913 71.461 74.408 0.750 re f
433.913 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 77.488 Td /F1 9.8 Tf  [(56.33)] TJ ET
0.267 0.267 0.267 rg
507.571 87.343 73.304 0.750 re f
507.571 71.461 73.304 0.750 re f
507.571 71.461 0.750 16.631 re f
580.125 71.461 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 77.488 Td /F1 9.8 Tf  [(52.04)] TJ ET
Q
q
0.000 0.000 0.000 rg
BT 291.710 19.825 Td /F1 11.0 Tf  [(6)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

Q
endstream
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>>
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0.271 0.267 0.267 rg
q
15.000 30.532 577.500 746.468 re W n
1.000 1.000 1.000 rg
26.250 729.112 555.000 47.888 re f
0.267 0.267 0.267 rg
26.625 776.625 193.482 0.750 re f
26.625 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 31.875 766.770 Td /F1 9.8 Tf  [(ClustalW-quicktree)] TJ ET
0.267 0.267 0.267 rg
219.357 776.625 99.216 0.750 re f
219.357 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 224.607 766.770 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
317.823 776.625 116.840 0.750 re f
317.823 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 323.073 766.770 Td /F1 9.8 Tf  [(54.37)] TJ ET
0.267 0.267 0.267 rg
433.913 776.625 74.408 0.750 re f
433.913 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 439.163 766.770 Td /F1 9.8 Tf  [(63.03)] TJ ET
0.267 0.267 0.267 rg
507.571 776.625 73.304 0.750 re f
507.571 745.369 0.750 32.006 re f
580.125 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 512.821 766.770 Td /F1 9.8 Tf  [(52.84)] TJ ET
0.267 0.267 0.267 rg
26.625 745.369 193.482 0.750 re f
26.625 729.487 193.482 0.750 re f
26.625 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 735.514 Td /F1 9.8 Tf  [(Opal)] TJ ET
0.267 0.267 0.267 rg
219.357 745.369 99.216 0.750 re f
219.357 729.487 99.216 0.750 re f
219.357 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 735.514 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 745.369 116.840 0.750 re f
317.823 729.487 116.840 0.750 re f
317.823 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 735.514 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 745.369 74.408 0.750 re f
433.913 729.487 74.408 0.750 re f
433.913 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 735.514 Td /F1 9.8 Tf  [(39.33)] TJ ET
0.267 0.267 0.267 rg
507.571 745.369 73.304 0.750 re f
507.571 729.487 73.304 0.750 re f
507.571 729.487 0.750 16.631 re f
580.125 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 735.514 Td /F1 9.8 Tf  [(F)] TJ ET
BT 26.250 682.089 Td /F4 9.8 Tf  [(Table 5:)] TJ ET
BT 63.095 682.089 Td /F4 9.8 Tf  [( Runtimes \(in hours\) for each method on each of the four largest datasets.)] TJ ET
BT 406.578 682.089 Td /F1 9.8 Tf  [( Each row lists results for a method, )] TJ ET
BT 26.250 670.184 Td /F1 9.8 Tf  [(and each column corresponds to a dataset. ML tree estimation performed using RAxML for all alignments with the exception of )] TJ ET
BT 26.250 658.279 Td /F1 9.8 Tf  [(alignments estimated for the Price 78K dataset; we note this by using the prefix �FT:� before the missing branch rate for the )] TJ ET
BT 26.250 646.374 Td /F1 9.8 Tf  [(Price 78K dataset. �F� indicates that the method aborted on the dataset. �s.r� indicates that the method was still running at the )] TJ ET
BT 26.250 634.470 Td /F1 9.8 Tf  [(time of submission of this manuscript on a machine with 256 GB main memory. Entry �n.a� indicates a method that we did not )] TJ ET
BT 26.250 622.565 Td /F1 9.8 Tf  [(attempt to run. The Appendix provides further details about the hardware used for these computations.)] TJ ET
BT 26.250 585.962 Td /F4 12.0 Tf  [(Discussion)] TJ ET
BT 26.250 566.008 Td /F1 9.8 Tf  [(hese analyses show that the choice of alignment method has a very large impact on phylogenetic accuracy. On the datasets )] TJ ET
BT 26.250 554.103 Td /F1 9.8 Tf  [(with at most \(about\) 1000 sequences, all the alignment methods can be run, although they differ substantially in terms of )] TJ ET
BT 26.250 542.199 Td /F1 9.8 Tf  [(alignment and tree accuracy, as well as in terms of computational requirements. More specifically, highly accurate trees and )] TJ ET
BT 26.250 530.294 Td /F1 9.8 Tf  [(alignments can be computed on the smaller datasets \(up to approximately 1000 sequences\), provided that the most accurate )] TJ ET
BT 26.250 518.389 Td /F1 9.8 Tf  [(alignment and tree estimation methods are used \(i.e., RAxML on the default MAFFT alignment, or SAT�\). By contrast, the other )] TJ ET
BT 26.250 506.484 Td /F1 9.8 Tf  [(alignment methods we tested produced alignments that were much less accurate, so that trees estimated on these alignments )] TJ ET
BT 26.250 494.580 Td /F1 9.8 Tf  [(also had much higher error rates. Finally, although all methods were successfully able to complete their analyses with at most 4 )] TJ ET
BT 26.250 482.675 Td /F1 9.8 Tf  [(GB of main memory, many alignment methods took about 10 hours to run on many of these datsets, so that alignment )] TJ ET
BT 26.250 470.770 Td /F1 9.8 Tf  [(estimation took more time than phylogeny estimation in some cases.)] TJ ET
BT 26.250 451.365 Td /F1 9.8 Tf  [(On the larger datasets, with upwards of 6,000 sequences, the analyses show that most methods are unable to run, even when )] TJ ET
BT 26.250 439.461 Td /F1 9.8 Tf  [(provided with very large amounts of main memory; instead, only the Quicktree option within ClustalW and the PartTree option )] TJ ET
BT 26.250 427.556 Td /F1 9.8 Tf  [(with MAFFT were able to complete analyses on all the datasets we studied with 6,000 to 28,000 sequences \(although some )] TJ ET
BT 26.250 415.651 Td /F1 9.8 Tf  [(methods are still running\), and PartTree was the only method that succeeded on the largest dataset, with 78,132 sequences. )] TJ ET
BT 26.250 403.746 Td /F1 9.8 Tf  [(Running times on the largest datasets were substantial, anywhere from several days to several weeks, just to obtain the )] TJ ET
BT 26.250 391.842 Td /F1 9.8 Tf  [(sequence alignment \(i.e., not counting the tree estimation step\). Memory requirements were also high, as many methods could )] TJ ET
BT 26.250 379.937 Td /F1 9.8 Tf  [(not run even when given dedicated access to all 32 GB of main memory on a machine, and had to be run on machines with )] TJ ET
BT 26.250 368.032 Td /F1 9.8 Tf  [(more memory.)] TJ ET
BT 26.250 348.627 Td /F1 9.8 Tf  [(One of the interesting outcomes of this study is the observation that two methods � PartTree and QuickTree � are both able to )] TJ ET
BT 26.250 336.723 Td /F1 9.8 Tf  [(analyze many large datasets. Even these methods, however, can be computationally intensive on large datasets. For example, )] TJ ET
BT 26.250 324.818 Td /F1 9.8 Tf  [(on the 16S.B.ALL dataset, with almost 28,000 sequences, QuickTree used about a week and PartTree used almost 11 days. )] TJ ET
BT 26.250 312.913 Td /F1 9.8 Tf  [(Unfortunately, neither Quicktree nor PartTree is reliable in terms of alignment accuracy: the ML tree on the QuickTree alignment )] TJ ET
BT 26.250 301.008 Td /F1 9.8 Tf  [(of the 16S.T dataset had 34% missing branch rate, and the ML tree on the PartTree alignment of the 16S.B.ALL dataset had )] TJ ET
BT 26.250 289.104 Td /F1 9.8 Tf  [(32% missing branch rate. Thus, the alignment methods that can be run on large datasets are not reliably accurate, and )] TJ ET
BT 26.250 277.199 Td /F1 9.8 Tf  [(phylogenies based upon these alignments can have high error.)] TJ ET
BT 26.250 257.794 Td /F1 9.8 Tf  [(Finally, we note that these results show that evaluating alignment accuracy using the SP-FN measure is not necessarily )] TJ ET
BT 26.250 245.889 Td /F1 9.8 Tf  [(predictive of phylogenetic accuracy. For example, ML trees on Prank+GT alignments have reasonably low missing branch rates )] TJ ET
BT 26.250 233.985 Td /F1 9.8 Tf  [(although Prank+GT alignments have high SP-FN error, and ML trees on Opal alignments have high missing branch rates, )] TJ ET
BT 26.250 222.080 Td /F1 9.8 Tf  [(although Opal alignments have low SP-FN error. Hence, evaluations of alignment methods in terms of their consequences for )] TJ ET
BT 26.250 210.175 Td /F1 9.8 Tf  [(phylogenetic accuracy must be performed with care.)] TJ ET
BT 26.250 190.770 Td /F4 9.8 Tf  [(Conclusions)] TJ ET
BT 26.250 171.366 Td /F1 9.8 Tf  [(This study shows that highly accurate alignments can be estimated when the datasets are small enough \(at most a few )] TJ ET
BT 26.250 159.461 Td /F1 9.8 Tf  [(thousand sequences\) and only the best methods are used \(e.g., SAT� and MAFFT\), or when the sequences have evolved )] TJ ET
BT 26.250 147.556 Td /F1 9.8 Tf  [(under sufficiently low rates of indels. However, under other conditions, such as datasets with tens of thousands of sequences, )] TJ ET
BT 26.250 135.651 Td /F1 9.8 Tf  [(very few alignment methods can even run at all, even when run on machines with very large memories. Furthermore, the )] TJ ET
BT 26.250 123.747 Td /F1 9.8 Tf  [(alignment methods that can be run on the very largest datasets \(i.e., PartTree and QuickTree\) are not methods with high )] TJ ET
BT 26.250 111.842 Td /F1 9.8 Tf  [(accuracy. While accurate alignments can still be computed using these methods if the datasets have almost no indels, )] TJ ET
BT 26.250 99.937 Td /F1 9.8 Tf  [(alignments estimated when indels are present will generally be poor. The consequence is that maximum likelihood trees )] TJ ET
BT 26.250 88.032 Td /F1 9.8 Tf  [(estimated on these alignments will be far from highly accurate. Since maximum likelihood tree estimation has become the )] TJ ET
BT 26.250 76.128 Td /F1 9.8 Tf  [(dominant method for use in large-scale phylogenetic studies, this study shows that trees estimated on alignments of single )] TJ ET
BT 26.250 64.223 Td /F1 9.8 Tf  [(genes will be likely to fail to recover many of the well-supported edges of trees estimated on the true alignments.)] TJ ET
BT 26.250 44.818 Td /F1 9.8 Tf  [(What are the consequences of this study for large-scale phylogenetic estimation? Our study shows clearly that alignments of )] TJ ET
Q
q
15.000 30.532 577.500 746.468 re W n
1.000 1.000 1.000 rg
26.250 729.112 555.000 47.888 re f
0.267 0.267 0.267 rg
26.625 776.625 193.482 0.750 re f
26.625 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 31.875 766.770 Td /F1 9.8 Tf  [(ClustalW-quicktree)] TJ ET
0.267 0.267 0.267 rg
219.357 776.625 99.216 0.750 re f
219.357 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 224.607 766.770 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
317.823 776.625 116.840 0.750 re f
317.823 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 323.073 766.770 Td /F1 9.8 Tf  [(54.37)] TJ ET
0.267 0.267 0.267 rg
433.913 776.625 74.408 0.750 re f
433.913 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 439.163 766.770 Td /F1 9.8 Tf  [(63.03)] TJ ET
0.267 0.267 0.267 rg
507.571 776.625 73.304 0.750 re f
507.571 745.369 0.750 32.006 re f
580.125 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 512.821 766.770 Td /F1 9.8 Tf  [(52.84)] TJ ET
0.267 0.267 0.267 rg
26.625 745.369 193.482 0.750 re f
26.625 729.487 193.482 0.750 re f
26.625 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 735.514 Td /F1 9.8 Tf  [(Opal)] TJ ET
0.267 0.267 0.267 rg
219.357 745.369 99.216 0.750 re f
219.357 729.487 99.216 0.750 re f
219.357 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 735.514 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 745.369 116.840 0.750 re f
317.823 729.487 116.840 0.750 re f
317.823 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 735.514 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 745.369 74.408 0.750 re f
433.913 729.487 74.408 0.750 re f
433.913 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 735.514 Td /F1 9.8 Tf  [(39.33)] TJ ET
0.267 0.267 0.267 rg
507.571 745.369 73.304 0.750 re f
507.571 729.487 73.304 0.750 re f
507.571 729.487 0.750 16.631 re f
580.125 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 735.514 Td /F1 9.8 Tf  [(F)] TJ ET
BT 26.250 682.089 Td /F4 9.8 Tf  [(Table 5:)] TJ ET
BT 63.095 682.089 Td /F4 9.8 Tf  [( Runtimes \(in hours\) for each method on each of the four largest datasets.)] TJ ET
BT 406.578 682.089 Td /F1 9.8 Tf  [( Each row lists results for a method, )] TJ ET
BT 26.250 670.184 Td /F1 9.8 Tf  [(and each column corresponds to a dataset. ML tree estimation performed using RAxML for all alignments with the exception of )] TJ ET
BT 26.250 658.279 Td /F1 9.8 Tf  [(alignments estimated for the Price 78K dataset; we note this by using the prefix �FT:� before the missing branch rate for the )] TJ ET
BT 26.250 646.374 Td /F1 9.8 Tf  [(Price 78K dataset. �F� indicates that the method aborted on the dataset. �s.r� indicates that the method was still running at the )] TJ ET
BT 26.250 634.470 Td /F1 9.8 Tf  [(time of submission of this manuscript on a machine with 256 GB main memory. Entry �n.a� indicates a method that we did not )] TJ ET
BT 26.250 622.565 Td /F1 9.8 Tf  [(attempt to run. The Appendix provides further details about the hardware used for these computations.)] TJ ET
BT 26.250 585.962 Td /F4 12.0 Tf  [(Discussion)] TJ ET
BT 26.250 566.008 Td /F1 9.8 Tf  [(hese analyses show that the choice of alignment method has a very large impact on phylogenetic accuracy. On the datasets )] TJ ET
BT 26.250 554.103 Td /F1 9.8 Tf  [(with at most \(about\) 1000 sequences, all the alignment methods can be run, although they differ substantially in terms of )] TJ ET
BT 26.250 542.199 Td /F1 9.8 Tf  [(alignment and tree accuracy, as well as in terms of computational requirements. More specifically, highly accurate trees and )] TJ ET
BT 26.250 530.294 Td /F1 9.8 Tf  [(alignments can be computed on the smaller datasets \(up to approximately 1000 sequences\), provided that the most accurate )] TJ ET
BT 26.250 518.389 Td /F1 9.8 Tf  [(alignment and tree estimation methods are used \(i.e., RAxML on the default MAFFT alignment, or SAT�\). By contrast, the other )] TJ ET
BT 26.250 506.484 Td /F1 9.8 Tf  [(alignment methods we tested produced alignments that were much less accurate, so that trees estimated on these alignments )] TJ ET
BT 26.250 494.580 Td /F1 9.8 Tf  [(also had much higher error rates. Finally, although all methods were successfully able to complete their analyses with at most 4 )] TJ ET
BT 26.250 482.675 Td /F1 9.8 Tf  [(GB of main memory, many alignment methods took about 10 hours to run on many of these datsets, so that alignment )] TJ ET
BT 26.250 470.770 Td /F1 9.8 Tf  [(estimation took more time than phylogeny estimation in some cases.)] TJ ET
BT 26.250 451.365 Td /F1 9.8 Tf  [(On the larger datasets, with upwards of 6,000 sequences, the analyses show that most methods are unable to run, even when )] TJ ET
BT 26.250 439.461 Td /F1 9.8 Tf  [(provided with very large amounts of main memory; instead, only the Quicktree option within ClustalW and the PartTree option )] TJ ET
BT 26.250 427.556 Td /F1 9.8 Tf  [(with MAFFT were able to complete analyses on all the datasets we studied with 6,000 to 28,000 sequences \(although some )] TJ ET
BT 26.250 415.651 Td /F1 9.8 Tf  [(methods are still running\), and PartTree was the only method that succeeded on the largest dataset, with 78,132 sequences. )] TJ ET
BT 26.250 403.746 Td /F1 9.8 Tf  [(Running times on the largest datasets were substantial, anywhere from several days to several weeks, just to obtain the )] TJ ET
BT 26.250 391.842 Td /F1 9.8 Tf  [(sequence alignment \(i.e., not counting the tree estimation step\). Memory requirements were also high, as many methods could )] TJ ET
BT 26.250 379.937 Td /F1 9.8 Tf  [(not run even when given dedicated access to all 32 GB of main memory on a machine, and had to be run on machines with )] TJ ET
BT 26.250 368.032 Td /F1 9.8 Tf  [(more memory.)] TJ ET
BT 26.250 348.627 Td /F1 9.8 Tf  [(One of the interesting outcomes of this study is the observation that two methods � PartTree and QuickTree � are both able to )] TJ ET
BT 26.250 336.723 Td /F1 9.8 Tf  [(analyze many large datasets. Even these methods, however, can be computationally intensive on large datasets. For example, )] TJ ET
BT 26.250 324.818 Td /F1 9.8 Tf  [(on the 16S.B.ALL dataset, with almost 28,000 sequences, QuickTree used about a week and PartTree used almost 11 days. )] TJ ET
BT 26.250 312.913 Td /F1 9.8 Tf  [(Unfortunately, neither Quicktree nor PartTree is reliable in terms of alignment accuracy: the ML tree on the QuickTree alignment )] TJ ET
BT 26.250 301.008 Td /F1 9.8 Tf  [(of the 16S.T dataset had 34% missing branch rate, and the ML tree on the PartTree alignment of the 16S.B.ALL dataset had )] TJ ET
BT 26.250 289.104 Td /F1 9.8 Tf  [(32% missing branch rate. Thus, the alignment methods that can be run on large datasets are not reliably accurate, and )] TJ ET
BT 26.250 277.199 Td /F1 9.8 Tf  [(phylogenies based upon these alignments can have high error.)] TJ ET
BT 26.250 257.794 Td /F1 9.8 Tf  [(Finally, we note that these results show that evaluating alignment accuracy using the SP-FN measure is not necessarily )] TJ ET
BT 26.250 245.889 Td /F1 9.8 Tf  [(predictive of phylogenetic accuracy. For example, ML trees on Prank+GT alignments have reasonably low missing branch rates )] TJ ET
BT 26.250 233.985 Td /F1 9.8 Tf  [(although Prank+GT alignments have high SP-FN error, and ML trees on Opal alignments have high missing branch rates, )] TJ ET
BT 26.250 222.080 Td /F1 9.8 Tf  [(although Opal alignments have low SP-FN error. Hence, evaluations of alignment methods in terms of their consequences for )] TJ ET
BT 26.250 210.175 Td /F1 9.8 Tf  [(phylogenetic accuracy must be performed with care.)] TJ ET
BT 26.250 190.770 Td /F4 9.8 Tf  [(Conclusions)] TJ ET
BT 26.250 171.366 Td /F1 9.8 Tf  [(This study shows that highly accurate alignments can be estimated when the datasets are small enough \(at most a few )] TJ ET
BT 26.250 159.461 Td /F1 9.8 Tf  [(thousand sequences\) and only the best methods are used \(e.g., SAT� and MAFFT\), or when the sequences have evolved )] TJ ET
BT 26.250 147.556 Td /F1 9.8 Tf  [(under sufficiently low rates of indels. However, under other conditions, such as datasets with tens of thousands of sequences, )] TJ ET
BT 26.250 135.651 Td /F1 9.8 Tf  [(very few alignment methods can even run at all, even when run on machines with very large memories. Furthermore, the )] TJ ET
BT 26.250 123.747 Td /F1 9.8 Tf  [(alignment methods that can be run on the very largest datasets \(i.e., PartTree and QuickTree\) are not methods with high )] TJ ET
BT 26.250 111.842 Td /F1 9.8 Tf  [(accuracy. While accurate alignments can still be computed using these methods if the datasets have almost no indels, )] TJ ET
BT 26.250 99.937 Td /F1 9.8 Tf  [(alignments estimated when indels are present will generally be poor. The consequence is that maximum likelihood trees )] TJ ET
BT 26.250 88.032 Td /F1 9.8 Tf  [(estimated on these alignments will be far from highly accurate. Since maximum likelihood tree estimation has become the )] TJ ET
BT 26.250 76.128 Td /F1 9.8 Tf  [(dominant method for use in large-scale phylogenetic studies, this study shows that trees estimated on alignments of single )] TJ ET
BT 26.250 64.223 Td /F1 9.8 Tf  [(genes will be likely to fail to recover many of the well-supported edges of trees estimated on the true alignments.)] TJ ET
BT 26.250 44.818 Td /F1 9.8 Tf  [(What are the consequences of this study for large-scale phylogenetic estimation? Our study shows clearly that alignments of )] TJ ET
Q
q
15.000 30.532 577.500 746.468 re W n
1.000 1.000 1.000 rg
26.250 729.112 555.000 47.888 re f
0.267 0.267 0.267 rg
26.625 776.625 193.482 0.750 re f
26.625 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 31.875 766.770 Td /F1 9.8 Tf  [(ClustalW-quicktree)] TJ ET
0.267 0.267 0.267 rg
219.357 776.625 99.216 0.750 re f
219.357 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 224.607 766.770 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
317.823 776.625 116.840 0.750 re f
317.823 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 323.073 766.770 Td /F1 9.8 Tf  [(54.37)] TJ ET
0.267 0.267 0.267 rg
433.913 776.625 74.408 0.750 re f
433.913 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 439.163 766.770 Td /F1 9.8 Tf  [(63.03)] TJ ET
0.267 0.267 0.267 rg
507.571 776.625 73.304 0.750 re f
507.571 745.369 0.750 32.006 re f
580.125 745.369 0.750 32.006 re f
0.271 0.267 0.267 rg
BT 512.821 766.770 Td /F1 9.8 Tf  [(52.84)] TJ ET
0.267 0.267 0.267 rg
26.625 745.369 193.482 0.750 re f
26.625 729.487 193.482 0.750 re f
26.625 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 31.875 735.514 Td /F1 9.8 Tf  [(Opal)] TJ ET
0.267 0.267 0.267 rg
219.357 745.369 99.216 0.750 re f
219.357 729.487 99.216 0.750 re f
219.357 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 224.607 735.514 Td /F1 9.8 Tf  [(n.a.)] TJ ET
0.267 0.267 0.267 rg
317.823 745.369 116.840 0.750 re f
317.823 729.487 116.840 0.750 re f
317.823 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 323.073 735.514 Td /F1 9.8 Tf  [(F)] TJ ET
0.267 0.267 0.267 rg
433.913 745.369 74.408 0.750 re f
433.913 729.487 74.408 0.750 re f
433.913 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 439.163 735.514 Td /F1 9.8 Tf  [(39.33)] TJ ET
0.267 0.267 0.267 rg
507.571 745.369 73.304 0.750 re f
507.571 729.487 73.304 0.750 re f
507.571 729.487 0.750 16.631 re f
580.125 729.487 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 512.821 735.514 Td /F1 9.8 Tf  [(F)] TJ ET
BT 26.250 682.089 Td /F4 9.8 Tf  [(Table 5:)] TJ ET
BT 63.095 682.089 Td /F4 9.8 Tf  [( Runtimes \(in hours\) for each method on each of the four largest datasets.)] TJ ET
BT 406.578 682.089 Td /F1 9.8 Tf  [( Each row lists results for a method, )] TJ ET
BT 26.250 670.184 Td /F1 9.8 Tf  [(and each column corresponds to a dataset. ML tree estimation performed using RAxML for all alignments with the exception of )] TJ ET
BT 26.250 658.279 Td /F1 9.8 Tf  [(alignments estimated for the Price 78K dataset; we note this by using the prefix �FT:� before the missing branch rate for the )] TJ ET
BT 26.250 646.374 Td /F1 9.8 Tf  [(Price 78K dataset. �F� indicates that the method aborted on the dataset. �s.r� indicates that the method was still running at the )] TJ ET
BT 26.250 634.470 Td /F1 9.8 Tf  [(time of submission of this manuscript on a machine with 256 GB main memory. Entry �n.a� indicates a method that we did not )] TJ ET
BT 26.250 622.565 Td /F1 9.8 Tf  [(attempt to run. The Appendix provides further details about the hardware used for these computations.)] TJ ET
BT 26.250 585.962 Td /F4 12.0 Tf  [(Discussion)] TJ ET
BT 26.250 566.008 Td /F1 9.8 Tf  [(hese analyses show that the choice of alignment method has a very large impact on phylogenetic accuracy. On the datasets )] TJ ET
BT 26.250 554.103 Td /F1 9.8 Tf  [(with at most \(about\) 1000 sequences, all the alignment methods can be run, although they differ substantially in terms of )] TJ ET
BT 26.250 542.199 Td /F1 9.8 Tf  [(alignment and tree accuracy, as well as in terms of computational requirements. More specifically, highly accurate trees and )] TJ ET
BT 26.250 530.294 Td /F1 9.8 Tf  [(alignments can be computed on the smaller datasets \(up to approximately 1000 sequences\), provided that the most accurate )] TJ ET
BT 26.250 518.389 Td /F1 9.8 Tf  [(alignment and tree estimation methods are used \(i.e., RAxML on the default MAFFT alignment, or SAT�\). By contrast, the other )] TJ ET
BT 26.250 506.484 Td /F1 9.8 Tf  [(alignment methods we tested produced alignments that were much less accurate, so that trees estimated on these alignments )] TJ ET
BT 26.250 494.580 Td /F1 9.8 Tf  [(also had much higher error rates. Finally, although all methods were successfully able to complete their analyses with at most 4 )] TJ ET
BT 26.250 482.675 Td /F1 9.8 Tf  [(GB of main memory, many alignment methods took about 10 hours to run on many of these datsets, so that alignment )] TJ ET
BT 26.250 470.770 Td /F1 9.8 Tf  [(estimation took more time than phylogeny estimation in some cases.)] TJ ET
BT 26.250 451.365 Td /F1 9.8 Tf  [(On the larger datasets, with upwards of 6,000 sequences, the analyses show that most methods are unable to run, even when )] TJ ET
BT 26.250 439.461 Td /F1 9.8 Tf  [(provided with very large amounts of main memory; instead, only the Quicktree option within ClustalW and the PartTree option )] TJ ET
BT 26.250 427.556 Td /F1 9.8 Tf  [(with MAFFT were able to complete analyses on all the datasets we studied with 6,000 to 28,000 sequences \(although some )] TJ ET
BT 26.250 415.651 Td /F1 9.8 Tf  [(methods are still running\), and PartTree was the only method that succeeded on the largest dataset, with 78,132 sequences. )] TJ ET
BT 26.250 403.746 Td /F1 9.8 Tf  [(Running times on the largest datasets were substantial, anywhere from several days to several weeks, just to obtain the )] TJ ET
BT 26.250 391.842 Td /F1 9.8 Tf  [(sequence alignment \(i.e., not counting the tree estimation step\). Memory requirements were also high, as many methods could )] TJ ET
BT 26.250 379.937 Td /F1 9.8 Tf  [(not run even when given dedicated access to all 32 GB of main memory on a machine, and had to be run on machines with )] TJ ET
BT 26.250 368.032 Td /F1 9.8 Tf  [(more memory.)] TJ ET
BT 26.250 348.627 Td /F1 9.8 Tf  [(One of the interesting outcomes of this study is the observation that two methods � PartTree and QuickTree � are both able to )] TJ ET
BT 26.250 336.723 Td /F1 9.8 Tf  [(analyze many large datasets. Even these methods, however, can be computationally intensive on large datasets. For example, )] TJ ET
BT 26.250 324.818 Td /F1 9.8 Tf  [(on the 16S.B.ALL dataset, with almost 28,000 sequences, QuickTree used about a week and PartTree used almost 11 days. )] TJ ET
BT 26.250 312.913 Td /F1 9.8 Tf  [(Unfortunately, neither Quicktree nor PartTree is reliable in terms of alignment accuracy: the ML tree on the QuickTree alignment )] TJ ET
BT 26.250 301.008 Td /F1 9.8 Tf  [(of the 16S.T dataset had 34% missing branch rate, and the ML tree on the PartTree alignment of the 16S.B.ALL dataset had )] TJ ET
BT 26.250 289.104 Td /F1 9.8 Tf  [(32% missing branch rate. Thus, the alignment methods that can be run on large datasets are not reliably accurate, and )] TJ ET
BT 26.250 277.199 Td /F1 9.8 Tf  [(phylogenies based upon these alignments can have high error.)] TJ ET
BT 26.250 257.794 Td /F1 9.8 Tf  [(Finally, we note that these results show that evaluating alignment accuracy using the SP-FN measure is not necessarily )] TJ ET
BT 26.250 245.889 Td /F1 9.8 Tf  [(predictive of phylogenetic accuracy. For example, ML trees on Prank+GT alignments have reasonably low missing branch rates )] TJ ET
BT 26.250 233.985 Td /F1 9.8 Tf  [(although Prank+GT alignments have high SP-FN error, and ML trees on Opal alignments have high missing branch rates, )] TJ ET
BT 26.250 222.080 Td /F1 9.8 Tf  [(although Opal alignments have low SP-FN error. Hence, evaluations of alignment methods in terms of their consequences for )] TJ ET
BT 26.250 210.175 Td /F1 9.8 Tf  [(phylogenetic accuracy must be performed with care.)] TJ ET
BT 26.250 190.770 Td /F4 9.8 Tf  [(Conclusions)] TJ ET
BT 26.250 171.366 Td /F1 9.8 Tf  [(This study shows that highly accurate alignments can be estimated when the datasets are small enough \(at most a few )] TJ ET
BT 26.250 159.461 Td /F1 9.8 Tf  [(thousand sequences\) and only the best methods are used \(e.g., SAT� and MAFFT\), or when the sequences have evolved )] TJ ET
BT 26.250 147.556 Td /F1 9.8 Tf  [(under sufficiently low rates of indels. However, under other conditions, such as datasets with tens of thousands of sequences, )] TJ ET
BT 26.250 135.651 Td /F1 9.8 Tf  [(very few alignment methods can even run at all, even when run on machines with very large memories. Furthermore, the )] TJ ET
BT 26.250 123.747 Td /F1 9.8 Tf  [(alignment methods that can be run on the very largest datasets \(i.e., PartTree and QuickTree\) are not methods with high )] TJ ET
BT 26.250 111.842 Td /F1 9.8 Tf  [(accuracy. While accurate alignments can still be computed using these methods if the datasets have almost no indels, )] TJ ET
BT 26.250 99.937 Td /F1 9.8 Tf  [(alignments estimated when indels are present will generally be poor. The consequence is that maximum likelihood trees )] TJ ET
BT 26.250 88.032 Td /F1 9.8 Tf  [(estimated on these alignments will be far from highly accurate. Since maximum likelihood tree estimation has become the )] TJ ET
BT 26.250 76.128 Td /F1 9.8 Tf  [(dominant method for use in large-scale phylogenetic studies, this study shows that trees estimated on alignments of single )] TJ ET
BT 26.250 64.223 Td /F1 9.8 Tf  [(genes will be likely to fail to recover many of the well-supported edges of trees estimated on the true alignments.)] TJ ET
BT 26.250 44.818 Td /F1 9.8 Tf  [(What are the consequences of this study for large-scale phylogenetic estimation? Our study shows clearly that alignments of )] TJ ET
Q
q
0.000 0.000 0.000 rg
BT 291.710 19.825 Td /F1 11.0 Tf  [(7)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

Q
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0.271 0.267 0.267 rg
q
15.000 34.473 577.500 742.527 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(large datasets that have evolved with many indels will likely have high error rates, and so gene trees estimated from these )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(alignments will also have high error. At a minimum, this means that the input to species tree estimations \(either concatenations )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(of estimated alignments or collections of estimated gene trees\) will have high error. This suggests that both of the dominant )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(ways of estimating species trees�either computing trees on concatenated alignments or combining gene tree estimates into a )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(species tree�are likely to have difficulty in producing accurate species tree estimates. Thus, the consequence for Tree of Life )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(studies is potentially serious.)] TJ ET
BT 26.250 688.548 Td /F1 9.8 Tf  [(In summary, the failure of alignment methods to be able to produce highly accurate alignments on large datasets is a limiting )] TJ ET
BT 26.250 676.643 Td /F1 9.8 Tf  [(factor in phylogenetic estimation, possibly greater than those confronting phylogeny estimation when the true alignment is given. )] TJ ET
BT 26.250 664.738 Td /F1 9.8 Tf  [(Clearly, new methods need to be developed to enable highly accurate alignment estimation for large datasets, or to construct )] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(trees without depending upon multiple sequence alignments of very large datasets.)] TJ ET
BT 26.250 616.231 Td /F4 12.0 Tf  [(Competing Interests)] TJ ET
BT 26.250 596.277 Td /F1 9.8 Tf  [(The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 559.674 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 539.720 Td /F1 9.8 Tf  [(We thank TACC \(The Texas Advanced Computing Center\) at the University of Texas for assistance in analyzing the 16S.B.ALL )] TJ ET
BT 26.250 527.815 Td /F1 9.8 Tf  [(dataset.)] TJ ET
BT 26.250 498.713 Td /F4 12.0 Tf  [(APPENDIX 1)] TJ ET
BT 26.250 478.758 Td /F4 9.8 Tf  [(Software versions and commands)] TJ ET
BT 26.250 459.354 Td /F4 9.8 Tf  [(Alignment methods)] TJ ET
BT 26.250 439.949 Td /F1 9.8 Tf  [(We used ClustalW version 2.0.4, MAFFT version 6.240, Muscle version 3.7, Prank+GT using Prank version 080904, and Opal )] TJ ET
BT 26.250 428.044 Td /F1 9.8 Tf  [(version 1.0.2, which required Java version 1.6.0_02.)] TJ ET
BT 26.250 408.639 Td /F1 9.8 Tf  [(In the commands for each method, given below, <input> is a FASTA-formatted input file containing unaligned sequences and )] TJ ET
BT 26.250 396.735 Td /F1 9.8 Tf  [(<output> is the resulting FASTA-formatted output file.)] TJ ET
0.271 0.267 0.267 RG
40.337 380.297 m 
40.337 380.744 40.154 381.188 39.838 381.504 c
39.522 381.820 39.078 382.004 38.631 382.004 c
38.185 382.004 37.741 381.820 37.425 381.504 c
37.109 381.188 36.925 380.744 36.925 380.297 c
36.925 379.851 37.109 379.407 37.425 379.091 c
37.741 378.775 38.185 378.591 38.631 378.591 c
39.078 378.591 39.522 378.775 39.838 379.091 c
40.154 379.407 40.337 379.851 40.337 380.297 c f
BT 45.750 377.330 Td /F1 9.8 Tf  [(Clustal W:)] TJ ET
BT 26.250 354.175 Td /F1 9.8 Tf  [(��� clustalw2 -align -infile=<input>)] TJ ET
BT 26.250 334.770 Td /F1 9.8 Tf  [(��� -outfile=<output> -output=fasta)] TJ ET
40.337 318.333 m 
40.337 318.780 40.154 319.224 39.838 319.540 c
39.522 319.856 39.078 320.040 38.631 320.040 c
38.185 320.040 37.741 319.856 37.425 319.540 c
37.109 319.224 36.925 318.780 36.925 318.333 c
36.925 317.887 37.109 317.443 37.425 317.127 c
37.741 316.811 38.185 316.627 38.631 316.627 c
39.078 316.627 39.522 316.811 39.838 317.127 c
40.154 317.443 40.337 317.887 40.337 318.333 c f
BT 45.750 315.366 Td /F1 9.8 Tf  [(ClustalW-Quicktree:)] TJ ET
BT 26.250 292.211 Td /F1 9.8 Tf  [(��� clustalw2 -align -infile=<input>)] TJ ET
BT 26.250 272.806 Td /F1 9.8 Tf  [(���� -outfile=<output> -output=fasta)] TJ ET
BT 26.250 253.401 Td /F1 9.8 Tf  [(���� -quicktree)] TJ ET
40.337 236.964 m 
40.337 237.411 40.154 237.855 39.838 238.171 c
39.522 238.487 39.078 238.671 38.631 238.671 c
38.185 238.671 37.741 238.487 37.425 238.171 c
37.109 237.855 36.925 237.411 36.925 236.964 c
36.925 236.518 37.109 236.074 37.425 235.758 c
37.741 235.442 38.185 235.258 38.631 235.258 c
39.078 235.258 39.522 235.442 39.838 235.758 c
40.154 236.074 40.337 236.518 40.337 236.964 c f
BT 45.750 233.997 Td /F1 9.8 Tf  [(MAFFT L-insi-i:)] TJ ET
BT 26.250 210.842 Td /F1 9.8 Tf  [(��� mafft --localpair --maxiterate 1000)] TJ ET
BT 26.250 191.437 Td /F1 9.8 Tf  [(��� --quiet <input> > <output>)] TJ ET
40.337 175.000 m 
40.337 175.447 40.154 175.891 39.838 176.207 c
39.522 176.522 39.078 176.706 38.631 176.706 c
38.185 176.706 37.741 176.522 37.425 176.207 c
37.109 175.891 36.925 175.447 36.925 175.000 c
36.925 174.553 37.109 174.109 37.425 173.793 c
37.741 173.478 38.185 173.294 38.631 173.294 c
39.078 173.294 39.522 173.478 39.838 173.793 c
40.154 174.109 40.337 174.553 40.337 175.000 c f
BT 45.750 172.032 Td /F1 9.8 Tf  [(MAFFT-PartTree:)] TJ ET
BT 26.250 148.878 Td /F1 9.8 Tf  [(��� mafft --parttree --retree 2)] TJ ET
BT 26.250 129.473 Td /F1 9.8 Tf  [(��� --partsize 1000 <input> > <output>)] TJ ET
40.337 113.036 m 
40.337 113.482 40.154 113.926 39.838 114.242 c
39.522 114.558 39.078 114.742 38.631 114.742 c
38.185 114.742 37.741 114.558 37.425 114.242 c
37.109 113.926 36.925 113.482 36.925 113.036 c
36.925 112.589 37.109 112.145 37.425 111.829 c
37.741 111.513 38.185 111.330 38.631 111.330 c
39.078 111.330 39.522 111.513 39.838 111.829 c
40.154 112.145 40.337 112.589 40.337 113.036 c f
BT 45.750 110.068 Td /F1 9.8 Tf  [(Muscle:)] TJ ET
BT 26.250 86.913 Td /F1 9.8 Tf  [(��� muscle -in <input> -out <output> -quiet)] TJ ET
40.337 70.476 m 
40.337 70.923 40.154 71.367 39.838 71.683 c
39.522 71.999 39.078 72.183 38.631 72.183 c
38.185 72.183 37.741 71.999 37.425 71.683 c
37.109 71.367 36.925 70.923 36.925 70.476 c
36.925 70.030 37.109 69.586 37.425 69.270 c
37.741 68.954 38.185 68.770 38.631 68.770 c
39.078 68.770 39.522 68.954 39.838 69.270 c
40.154 69.586 40.337 70.030 40.337 70.476 c f
BT 45.750 67.509 Td /F1 9.8 Tf  [(Prank+GT:)] TJ ET
Q
q
15.000 34.473 577.500 742.527 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(large datasets that have evolved with many indels will likely have high error rates, and so gene trees estimated from these )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(alignments will also have high error. At a minimum, this means that the input to species tree estimations \(either concatenations )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(of estimated alignments or collections of estimated gene trees\) will have high error. This suggests that both of the dominant )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(ways of estimating species trees�either computing trees on concatenated alignments or combining gene tree estimates into a )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(species tree�are likely to have difficulty in producing accurate species tree estimates. Thus, the consequence for Tree of Life )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(studies is potentially serious.)] TJ ET
BT 26.250 688.548 Td /F1 9.8 Tf  [(In summary, the failure of alignment methods to be able to produce highly accurate alignments on large datasets is a limiting )] TJ ET
BT 26.250 676.643 Td /F1 9.8 Tf  [(factor in phylogenetic estimation, possibly greater than those confronting phylogeny estimation when the true alignment is given. )] TJ ET
BT 26.250 664.738 Td /F1 9.8 Tf  [(Clearly, new methods need to be developed to enable highly accurate alignment estimation for large datasets, or to construct )] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(trees without depending upon multiple sequence alignments of very large datasets.)] TJ ET
BT 26.250 616.231 Td /F4 12.0 Tf  [(Competing Interests)] TJ ET
BT 26.250 596.277 Td /F1 9.8 Tf  [(The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 559.674 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 539.720 Td /F1 9.8 Tf  [(We thank TACC \(The Texas Advanced Computing Center\) at the University of Texas for assistance in analyzing the 16S.B.ALL )] TJ ET
BT 26.250 527.815 Td /F1 9.8 Tf  [(dataset.)] TJ ET
BT 26.250 498.713 Td /F4 12.0 Tf  [(APPENDIX 1)] TJ ET
BT 26.250 478.758 Td /F4 9.8 Tf  [(Software versions and commands)] TJ ET
BT 26.250 459.354 Td /F4 9.8 Tf  [(Alignment methods)] TJ ET
BT 26.250 439.949 Td /F1 9.8 Tf  [(We used ClustalW version 2.0.4, MAFFT version 6.240, Muscle version 3.7, Prank+GT using Prank version 080904, and Opal )] TJ ET
BT 26.250 428.044 Td /F1 9.8 Tf  [(version 1.0.2, which required Java version 1.6.0_02.)] TJ ET
BT 26.250 408.639 Td /F1 9.8 Tf  [(In the commands for each method, given below, <input> is a FASTA-formatted input file containing unaligned sequences and )] TJ ET
BT 26.250 396.735 Td /F1 9.8 Tf  [(<output> is the resulting FASTA-formatted output file.)] TJ ET
0.271 0.267 0.267 RG
40.337 380.297 m 
40.337 380.744 40.154 381.188 39.838 381.504 c
39.522 381.820 39.078 382.004 38.631 382.004 c
38.185 382.004 37.741 381.820 37.425 381.504 c
37.109 381.188 36.925 380.744 36.925 380.297 c
36.925 379.851 37.109 379.407 37.425 379.091 c
37.741 378.775 38.185 378.591 38.631 378.591 c
39.078 378.591 39.522 378.775 39.838 379.091 c
40.154 379.407 40.337 379.851 40.337 380.297 c f
BT 45.750 377.330 Td /F1 9.8 Tf  [(Clustal W:)] TJ ET
BT 26.250 354.175 Td /F1 9.8 Tf  [(��� clustalw2 -align -infile=<input>)] TJ ET
BT 26.250 334.770 Td /F1 9.8 Tf  [(��� -outfile=<output> -output=fasta)] TJ ET
40.337 318.333 m 
40.337 318.780 40.154 319.224 39.838 319.540 c
39.522 319.856 39.078 320.040 38.631 320.040 c
38.185 320.040 37.741 319.856 37.425 319.540 c
37.109 319.224 36.925 318.780 36.925 318.333 c
36.925 317.887 37.109 317.443 37.425 317.127 c
37.741 316.811 38.185 316.627 38.631 316.627 c
39.078 316.627 39.522 316.811 39.838 317.127 c
40.154 317.443 40.337 317.887 40.337 318.333 c f
BT 45.750 315.366 Td /F1 9.8 Tf  [(ClustalW-Quicktree:)] TJ ET
BT 26.250 292.211 Td /F1 9.8 Tf  [(��� clustalw2 -align -infile=<input>)] TJ ET
BT 26.250 272.806 Td /F1 9.8 Tf  [(���� -outfile=<output> -output=fasta)] TJ ET
BT 26.250 253.401 Td /F1 9.8 Tf  [(���� -quicktree)] TJ ET
40.337 236.964 m 
40.337 237.411 40.154 237.855 39.838 238.171 c
39.522 238.487 39.078 238.671 38.631 238.671 c
38.185 238.671 37.741 238.487 37.425 238.171 c
37.109 237.855 36.925 237.411 36.925 236.964 c
36.925 236.518 37.109 236.074 37.425 235.758 c
37.741 235.442 38.185 235.258 38.631 235.258 c
39.078 235.258 39.522 235.442 39.838 235.758 c
40.154 236.074 40.337 236.518 40.337 236.964 c f
BT 45.750 233.997 Td /F1 9.8 Tf  [(MAFFT L-insi-i:)] TJ ET
BT 26.250 210.842 Td /F1 9.8 Tf  [(��� mafft --localpair --maxiterate 1000)] TJ ET
BT 26.250 191.437 Td /F1 9.8 Tf  [(��� --quiet <input> > <output>)] TJ ET
40.337 175.000 m 
40.337 175.447 40.154 175.891 39.838 176.207 c
39.522 176.522 39.078 176.706 38.631 176.706 c
38.185 176.706 37.741 176.522 37.425 176.207 c
37.109 175.891 36.925 175.447 36.925 175.000 c
36.925 174.553 37.109 174.109 37.425 173.793 c
37.741 173.478 38.185 173.294 38.631 173.294 c
39.078 173.294 39.522 173.478 39.838 173.793 c
40.154 174.109 40.337 174.553 40.337 175.000 c f
BT 45.750 172.032 Td /F1 9.8 Tf  [(MAFFT-PartTree:)] TJ ET
BT 26.250 148.878 Td /F1 9.8 Tf  [(��� mafft --parttree --retree 2)] TJ ET
BT 26.250 129.473 Td /F1 9.8 Tf  [(��� --partsize 1000 <input> > <output>)] TJ ET
40.337 113.036 m 
40.337 113.482 40.154 113.926 39.838 114.242 c
39.522 114.558 39.078 114.742 38.631 114.742 c
38.185 114.742 37.741 114.558 37.425 114.242 c
37.109 113.926 36.925 113.482 36.925 113.036 c
36.925 112.589 37.109 112.145 37.425 111.829 c
37.741 111.513 38.185 111.330 38.631 111.330 c
39.078 111.330 39.522 111.513 39.838 111.829 c
40.154 112.145 40.337 112.589 40.337 113.036 c f
BT 45.750 110.068 Td /F1 9.8 Tf  [(Muscle:)] TJ ET
BT 26.250 86.913 Td /F1 9.8 Tf  [(��� muscle -in <input> -out <output> -quiet)] TJ ET
40.337 70.476 m 
40.337 70.923 40.154 71.367 39.838 71.683 c
39.522 71.999 39.078 72.183 38.631 72.183 c
38.185 72.183 37.741 71.999 37.425 71.683 c
37.109 71.367 36.925 70.923 36.925 70.476 c
36.925 70.030 37.109 69.586 37.425 69.270 c
37.741 68.954 38.185 68.770 38.631 68.770 c
39.078 68.770 39.522 68.954 39.838 69.270 c
40.154 69.586 40.337 70.030 40.337 70.476 c f
BT 45.750 67.509 Td /F1 9.8 Tf  [(Prank+GT:)] TJ ET
Q
q
15.000 34.473 577.500 742.527 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(large datasets that have evolved with many indels will likely have high error rates, and so gene trees estimated from these )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(alignments will also have high error. At a minimum, this means that the input to species tree estimations \(either concatenations )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(of estimated alignments or collections of estimated gene trees\) will have high error. This suggests that both of the dominant )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(ways of estimating species trees�either computing trees on concatenated alignments or combining gene tree estimates into a )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(species tree�are likely to have difficulty in producing accurate species tree estimates. Thus, the consequence for Tree of Life )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(studies is potentially serious.)] TJ ET
BT 26.250 688.548 Td /F1 9.8 Tf  [(In summary, the failure of alignment methods to be able to produce highly accurate alignments on large datasets is a limiting )] TJ ET
BT 26.250 676.643 Td /F1 9.8 Tf  [(factor in phylogenetic estimation, possibly greater than those confronting phylogeny estimation when the true alignment is given. )] TJ ET
BT 26.250 664.738 Td /F1 9.8 Tf  [(Clearly, new methods need to be developed to enable highly accurate alignment estimation for large datasets, or to construct )] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(trees without depending upon multiple sequence alignments of very large datasets.)] TJ ET
BT 26.250 616.231 Td /F4 12.0 Tf  [(Competing Interests)] TJ ET
BT 26.250 596.277 Td /F1 9.8 Tf  [(The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 559.674 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 539.720 Td /F1 9.8 Tf  [(We thank TACC \(The Texas Advanced Computing Center\) at the University of Texas for assistance in analyzing the 16S.B.ALL )] TJ ET
BT 26.250 527.815 Td /F1 9.8 Tf  [(dataset.)] TJ ET
BT 26.250 498.713 Td /F4 12.0 Tf  [(APPENDIX 1)] TJ ET
BT 26.250 478.758 Td /F4 9.8 Tf  [(Software versions and commands)] TJ ET
BT 26.250 459.354 Td /F4 9.8 Tf  [(Alignment methods)] TJ ET
BT 26.250 439.949 Td /F1 9.8 Tf  [(We used ClustalW version 2.0.4, MAFFT version 6.240, Muscle version 3.7, Prank+GT using Prank version 080904, and Opal )] TJ ET
BT 26.250 428.044 Td /F1 9.8 Tf  [(version 1.0.2, which required Java version 1.6.0_02.)] TJ ET
BT 26.250 408.639 Td /F1 9.8 Tf  [(In the commands for each method, given below, <input> is a FASTA-formatted input file containing unaligned sequences and )] TJ ET
BT 26.250 396.735 Td /F1 9.8 Tf  [(<output> is the resulting FASTA-formatted output file.)] TJ ET
0.271 0.267 0.267 RG
40.337 380.297 m 
40.337 380.744 40.154 381.188 39.838 381.504 c
39.522 381.820 39.078 382.004 38.631 382.004 c
38.185 382.004 37.741 381.820 37.425 381.504 c
37.109 381.188 36.925 380.744 36.925 380.297 c
36.925 379.851 37.109 379.407 37.425 379.091 c
37.741 378.775 38.185 378.591 38.631 378.591 c
39.078 378.591 39.522 378.775 39.838 379.091 c
40.154 379.407 40.337 379.851 40.337 380.297 c f
BT 45.750 377.330 Td /F1 9.8 Tf  [(Clustal W:)] TJ ET
BT 26.250 354.175 Td /F1 9.8 Tf  [(��� clustalw2 -align -infile=<input>)] TJ ET
BT 26.250 334.770 Td /F1 9.8 Tf  [(��� -outfile=<output> -output=fasta)] TJ ET
40.337 318.333 m 
40.337 318.780 40.154 319.224 39.838 319.540 c
39.522 319.856 39.078 320.040 38.631 320.040 c
38.185 320.040 37.741 319.856 37.425 319.540 c
37.109 319.224 36.925 318.780 36.925 318.333 c
36.925 317.887 37.109 317.443 37.425 317.127 c
37.741 316.811 38.185 316.627 38.631 316.627 c
39.078 316.627 39.522 316.811 39.838 317.127 c
40.154 317.443 40.337 317.887 40.337 318.333 c f
BT 45.750 315.366 Td /F1 9.8 Tf  [(ClustalW-Quicktree:)] TJ ET
BT 26.250 292.211 Td /F1 9.8 Tf  [(��� clustalw2 -align -infile=<input>)] TJ ET
BT 26.250 272.806 Td /F1 9.8 Tf  [(���� -outfile=<output> -output=fasta)] TJ ET
BT 26.250 253.401 Td /F1 9.8 Tf  [(���� -quicktree)] TJ ET
40.337 236.964 m 
40.337 237.411 40.154 237.855 39.838 238.171 c
39.522 238.487 39.078 238.671 38.631 238.671 c
38.185 238.671 37.741 238.487 37.425 238.171 c
37.109 237.855 36.925 237.411 36.925 236.964 c
36.925 236.518 37.109 236.074 37.425 235.758 c
37.741 235.442 38.185 235.258 38.631 235.258 c
39.078 235.258 39.522 235.442 39.838 235.758 c
40.154 236.074 40.337 236.518 40.337 236.964 c f
BT 45.750 233.997 Td /F1 9.8 Tf  [(MAFFT L-insi-i:)] TJ ET
BT 26.250 210.842 Td /F1 9.8 Tf  [(��� mafft --localpair --maxiterate 1000)] TJ ET
BT 26.250 191.437 Td /F1 9.8 Tf  [(��� --quiet <input> > <output>)] TJ ET
40.337 175.000 m 
40.337 175.447 40.154 175.891 39.838 176.207 c
39.522 176.522 39.078 176.706 38.631 176.706 c
38.185 176.706 37.741 176.522 37.425 176.207 c
37.109 175.891 36.925 175.447 36.925 175.000 c
36.925 174.553 37.109 174.109 37.425 173.793 c
37.741 173.478 38.185 173.294 38.631 173.294 c
39.078 173.294 39.522 173.478 39.838 173.793 c
40.154 174.109 40.337 174.553 40.337 175.000 c f
BT 45.750 172.032 Td /F1 9.8 Tf  [(MAFFT-PartTree:)] TJ ET
BT 26.250 148.878 Td /F1 9.8 Tf  [(��� mafft --parttree --retree 2)] TJ ET
BT 26.250 129.473 Td /F1 9.8 Tf  [(��� --partsize 1000 <input> > <output>)] TJ ET
40.337 113.036 m 
40.337 113.482 40.154 113.926 39.838 114.242 c
39.522 114.558 39.078 114.742 38.631 114.742 c
38.185 114.742 37.741 114.558 37.425 114.242 c
37.109 113.926 36.925 113.482 36.925 113.036 c
36.925 112.589 37.109 112.145 37.425 111.829 c
37.741 111.513 38.185 111.330 38.631 111.330 c
39.078 111.330 39.522 111.513 39.838 111.829 c
40.154 112.145 40.337 112.589 40.337 113.036 c f
BT 45.750 110.068 Td /F1 9.8 Tf  [(Muscle:)] TJ ET
BT 26.250 86.913 Td /F1 9.8 Tf  [(��� muscle -in <input> -out <output> -quiet)] TJ ET
40.337 70.476 m 
40.337 70.923 40.154 71.367 39.838 71.683 c
39.522 71.999 39.078 72.183 38.631 72.183 c
38.185 72.183 37.741 71.999 37.425 71.683 c
37.109 71.367 36.925 70.923 36.925 70.476 c
36.925 70.030 37.109 69.586 37.425 69.270 c
37.741 68.954 38.185 68.770 38.631 68.770 c
39.078 68.770 39.522 68.954 39.838 69.270 c
40.154 69.586 40.337 70.030 40.337 70.476 c f
BT 45.750 67.509 Td /F1 9.8 Tf  [(Prank+GT:)] TJ ET
Q
q
0.000 0.000 0.000 rg
BT 291.710 19.825 Td /F1 11.0 Tf  [(8)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

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0.271 0.267 0.267 rg
0.271 0.267 0.267 RG
q
15.000 44.500 577.500 732.500 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(��� prank -d=<input> -o=<output>)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(��� -t=<RAxML\(MAFFT\) guide tree> -noxml -notree)] TJ ET
BT 26.250 728.667 Td /F1 9.8 Tf  [(��� -nopost +F -matinitsize=5 -uselogs)] TJ ET
0.271 0.267 0.267 RG
40.337 712.230 m 
40.337 712.676 40.154 713.120 39.838 713.436 c
39.522 713.752 39.078 713.936 38.631 713.936 c
38.185 713.936 37.741 713.752 37.425 713.436 c
37.109 713.120 36.925 712.676 36.925 712.230 c
36.925 711.783 37.109 711.339 37.425 711.023 c
37.741 710.707 38.185 710.523 38.631 710.523 c
39.078 710.523 39.522 710.707 39.838 711.023 c
40.154 711.339 40.337 711.783 40.337 712.230 c f
BT 45.750 709.262 Td /F1 9.8 Tf  [(Opal:)] TJ ET
BT 26.250 686.107 Td /F1 9.8 Tf  [(��� java -jar Opal.1.0.2.jar --in <input>)] TJ ET
BT 26.250 666.702 Td /F1 9.8 Tf  [(��� --out <output>)] TJ ET
BT 26.250 647.298 Td /F4 9.8 Tf  [(Maximum likelihood estimation models)] TJ ET
BT 26.250 627.893 Td /F1 9.8 Tf  [(For all two-phase methods \(i.e., ML trees estimated on alignments other than in SAT�\), we computed the ML trees using either )] TJ ET
BT 26.250 615.988 Td /F1 9.8 Tf  [(RAxML version 7.0.4 or FastTree version 2.1.3, but FastTree was used only on the Price 78K dataset. All two-phase ML )] TJ ET
BT 26.250 604.083 Td /F1 9.8 Tf  [(estimations were run to completion.)] TJ ET
BT 26.250 584.679 Td /F1 9.8 Tf  [(The commands used are as follows \(<input> is a PHYLIP-formatted input alignment file\):)] TJ ET
40.337 568.241 m 
40.337 568.688 40.154 569.132 39.838 569.448 c
39.522 569.764 39.078 569.948 38.631 569.948 c
38.185 569.948 37.741 569.764 37.425 569.448 c
37.109 569.132 36.925 568.688 36.925 568.241 c
36.925 567.795 37.109 567.351 37.425 567.035 c
37.741 566.719 38.185 566.535 38.631 566.535 c
39.078 566.535 39.522 566.719 39.838 567.035 c
40.154 567.351 40.337 567.795 40.337 568.241 c f
BT 45.750 565.274 Td /F1 9.8 Tf  [(RAxML default:�������)] TJ ET
BT 26.250 542.119 Td /F1 9.8 Tf  [(��� raxmlHPC -m GTRMIX -w <work dir>)] TJ ET
BT 26.250 522.714 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -s <input>)] TJ ET
40.337 506.277 m 
40.337 506.724 40.154 507.168 39.838 507.484 c
39.522 507.800 39.078 507.983 38.631 507.983 c
38.185 507.983 37.741 507.800 37.425 507.484 c
37.109 507.168 36.925 506.724 36.925 506.277 c
36.925 505.831 37.109 505.387 37.425 505.071 c
37.741 504.755 38.185 504.571 38.631 504.571 c
39.078 504.571 39.522 504.755 39.838 505.071 c
40.154 505.387 40.337 505.831 40.337 506.277 c f
BT 45.750 503.310 Td /F1 9.8 Tf  [(FastTree:)] TJ ET
BT 26.250 480.155 Td /F1 9.8 Tf  [(��� FastTree -nt -gtr -nosupport)] TJ ET
BT 26.250 460.750 Td /F1 9.8 Tf  [(��� -log <log file> <input alignment> > <output tree>)] TJ ET
BT 26.250 441.345 Td /F1 9.8 Tf  [(�The use of RAxML within SAT� is also performed as given above, except for the three largest biological datasets. On these )] TJ ET
BT 26.250 429.441 Td /F1 9.8 Tf  [(datasets \(16S.B.ALL, 16S.T, and 16S.3\), the SAT� search utilized an alpha-version 7.2.4_sse3 of RAxML which makes use of a )] TJ ET
BT 26.250 417.536 Td /F1 9.8 Tf  [(stopping rule that permits faster runs than the default RAxML version 7.0.4 search.)] TJ ET
40.337 401.099 m 
40.337 401.545 40.154 401.989 39.838 402.305 c
39.522 402.621 39.078 402.805 38.631 402.805 c
38.185 402.805 37.741 402.621 37.425 402.305 c
37.109 401.989 36.925 401.545 36.925 401.099 c
36.925 400.652 37.109 400.208 37.425 399.892 c
37.741 399.576 38.185 399.392 38.631 399.392 c
39.078 399.392 39.522 399.576 39.838 399.892 c
40.154 400.208 40.337 400.652 40.337 401.099 c f
BT 45.750 398.131 Td /F1 9.8 Tf  [(RAxML alpha-version 7.2.4_sse3 fast search, used for SAT�:������)] TJ ET
BT 26.250 374.976 Td /F1 9.8 Tf  [(��� raxmlHPC-SSE3� -F -D -m GTRMIX)] TJ ET
BT 26.250 355.572 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -s <input>)] TJ ET
BT 26.250 336.167 Td /F1 9.8 Tf  [(Finally, for the purposes of constructing a reference tree on the biological datasets,�other than the three largest biological )] TJ ET
BT 26.250 324.262 Td /F1 9.8 Tf  [(datasets, we used the following�command in RAxML version 7.0.4 to estimate an ML tree on the curated alignment�and assign )] TJ ET
BT 26.250 312.357 Td /F1 9.8 Tf  [(support values to the edges of the ML tree using a rapid bootstrapping�analysis with 500 bootstrap replicates:)] TJ ET
40.337 295.920 m 
40.337 296.367 40.154 296.811 39.838 297.127 c
39.522 297.443 39.078 297.626 38.631 297.626 c
38.185 297.626 37.741 297.443 37.425 297.127 c
37.109 296.811 36.925 296.367 36.925 295.920 c
36.925 295.474 37.109 295.030 37.425 294.714 c
37.741 294.398 38.185 294.214 38.631 294.214 c
39.078 294.214 39.522 294.398 39.838 294.714 c
40.154 295.030 40.337 295.474 40.337 295.920 c f
BT 45.750 292.953 Td /F1 9.8 Tf  [(RAxML rapid bootstrap:����)] TJ ET
BT 26.250 269.798 Td /F1 9.8 Tf  [(��� raxmlHPC -f a -m GTRGAMMA -s <input>)] TJ ET
BT 26.250 250.393 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -x <random number>)] TJ ET
BT 26.250 230.988 Td /F1 9.8 Tf  [(��� -p <random number> -N <number of replicates>)] TJ ET
BT 26.250 211.584 Td /F1 9.8 Tf  [(To construct a reference tree on the 16S.3 and 16S.T datasets, we first estimated�an ML tree on the curated alignment using )] TJ ET
BT 26.250 199.679 Td /F1 9.8 Tf  [(RAxML version 7.2.6 with the RAxML�default command. Then, we performed a rapid bootstrap analysis to assign support�)] TJ ET
BT 26.250 187.774 Td /F1 9.8 Tf  [(values to the edges of the ML tree using RAxML version 7.0.4 with the RAxML rapid�bootstrap command. This analysis )] TJ ET
BT 26.250 175.869 Td /F1 9.8 Tf  [(consisted of 500 rapid bootstrap replicates for�the 16S.3 dataset and 346 rapid bootstrap replicates for the 16S.T dataset.)] TJ ET
BT 26.250 156.465 Td /F1 9.8 Tf  [(To construct a reference tree on the 16S.B.ALL dataset, we first estimated�an ML tree on the curated alignment using RAxML )] TJ ET
BT 26.250 144.560 Td /F1 9.8 Tf  [(version�7.0.4 with the RAxML default command. We then assigned support values to the�edges of the ML tree using 573 )] TJ ET
BT 26.250 132.655 Td /F1 9.8 Tf  [(bootstrap replicates from two different bootstrap�analyses.�129 out of the 573 bootstrap replicates were obtained using RAxML )] TJ ET
BT 26.250 120.750 Td /F1 9.8 Tf  [(version 7.0.4�with the RAxML rapid bootstrap command listed above.�444 out of the 573 bootstrap replicates were obtained )] TJ ET
BT 26.250 108.846 Td /F1 9.8 Tf  [(using RAxML version 7.2.5�to perform a standard�bootstrap analysis on TACC's Ranger supercomputer. RAxML was run in )] TJ ET
BT 26.250 96.941 Td /F1 9.8 Tf  [(parallel on�each bootstrap replicate using the four cores of a single compute node on Ranger�via the following command:)] TJ ET
40.337 80.504 m 
40.337 80.950 40.154 81.394 39.838 81.710 c
39.522 82.026 39.078 82.210 38.631 82.210 c
38.185 82.210 37.741 82.026 37.425 81.710 c
37.109 81.394 36.925 80.950 36.925 80.504 c
36.925 80.057 37.109 79.613 37.425 79.297 c
37.741 78.981 38.185 78.797 38.631 78.797 c
39.078 78.797 39.522 78.981 39.838 79.297 c
40.154 79.613 40.337 80.057 40.337 80.504 c f
BT 45.750 77.536 Td /F1 9.8 Tf  [(RAxML analysis of a single standard bootstrap replicate:)] TJ ET
BT 26.250 54.381 Td /F1 9.8 Tf  [(���� raxmlHPC-PTHREADS-SSE3 -m GTRCAT -s <input>)] TJ ET
Q
q
15.000 44.500 577.500 732.500 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(��� prank -d=<input> -o=<output>)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(��� -t=<RAxML\(MAFFT\) guide tree> -noxml -notree)] TJ ET
BT 26.250 728.667 Td /F1 9.8 Tf  [(��� -nopost +F -matinitsize=5 -uselogs)] TJ ET
0.271 0.267 0.267 RG
40.337 712.230 m 
40.337 712.676 40.154 713.120 39.838 713.436 c
39.522 713.752 39.078 713.936 38.631 713.936 c
38.185 713.936 37.741 713.752 37.425 713.436 c
37.109 713.120 36.925 712.676 36.925 712.230 c
36.925 711.783 37.109 711.339 37.425 711.023 c
37.741 710.707 38.185 710.523 38.631 710.523 c
39.078 710.523 39.522 710.707 39.838 711.023 c
40.154 711.339 40.337 711.783 40.337 712.230 c f
BT 45.750 709.262 Td /F1 9.8 Tf  [(Opal:)] TJ ET
BT 26.250 686.107 Td /F1 9.8 Tf  [(��� java -jar Opal.1.0.2.jar --in <input>)] TJ ET
BT 26.250 666.702 Td /F1 9.8 Tf  [(��� --out <output>)] TJ ET
BT 26.250 647.298 Td /F4 9.8 Tf  [(Maximum likelihood estimation models)] TJ ET
BT 26.250 627.893 Td /F1 9.8 Tf  [(For all two-phase methods \(i.e., ML trees estimated on alignments other than in SAT�\), we computed the ML trees using either )] TJ ET
BT 26.250 615.988 Td /F1 9.8 Tf  [(RAxML version 7.0.4 or FastTree version 2.1.3, but FastTree was used only on the Price 78K dataset. All two-phase ML )] TJ ET
BT 26.250 604.083 Td /F1 9.8 Tf  [(estimations were run to completion.)] TJ ET
BT 26.250 584.679 Td /F1 9.8 Tf  [(The commands used are as follows \(<input> is a PHYLIP-formatted input alignment file\):)] TJ ET
40.337 568.241 m 
40.337 568.688 40.154 569.132 39.838 569.448 c
39.522 569.764 39.078 569.948 38.631 569.948 c
38.185 569.948 37.741 569.764 37.425 569.448 c
37.109 569.132 36.925 568.688 36.925 568.241 c
36.925 567.795 37.109 567.351 37.425 567.035 c
37.741 566.719 38.185 566.535 38.631 566.535 c
39.078 566.535 39.522 566.719 39.838 567.035 c
40.154 567.351 40.337 567.795 40.337 568.241 c f
BT 45.750 565.274 Td /F1 9.8 Tf  [(RAxML default:�������)] TJ ET
BT 26.250 542.119 Td /F1 9.8 Tf  [(��� raxmlHPC -m GTRMIX -w <work dir>)] TJ ET
BT 26.250 522.714 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -s <input>)] TJ ET
40.337 506.277 m 
40.337 506.724 40.154 507.168 39.838 507.484 c
39.522 507.800 39.078 507.983 38.631 507.983 c
38.185 507.983 37.741 507.800 37.425 507.484 c
37.109 507.168 36.925 506.724 36.925 506.277 c
36.925 505.831 37.109 505.387 37.425 505.071 c
37.741 504.755 38.185 504.571 38.631 504.571 c
39.078 504.571 39.522 504.755 39.838 505.071 c
40.154 505.387 40.337 505.831 40.337 506.277 c f
BT 45.750 503.310 Td /F1 9.8 Tf  [(FastTree:)] TJ ET
BT 26.250 480.155 Td /F1 9.8 Tf  [(��� FastTree -nt -gtr -nosupport)] TJ ET
BT 26.250 460.750 Td /F1 9.8 Tf  [(��� -log <log file> <input alignment> > <output tree>)] TJ ET
BT 26.250 441.345 Td /F1 9.8 Tf  [(�The use of RAxML within SAT� is also performed as given above, except for the three largest biological datasets. On these )] TJ ET
BT 26.250 429.441 Td /F1 9.8 Tf  [(datasets \(16S.B.ALL, 16S.T, and 16S.3\), the SAT� search utilized an alpha-version 7.2.4_sse3 of RAxML which makes use of a )] TJ ET
BT 26.250 417.536 Td /F1 9.8 Tf  [(stopping rule that permits faster runs than the default RAxML version 7.0.4 search.)] TJ ET
40.337 401.099 m 
40.337 401.545 40.154 401.989 39.838 402.305 c
39.522 402.621 39.078 402.805 38.631 402.805 c
38.185 402.805 37.741 402.621 37.425 402.305 c
37.109 401.989 36.925 401.545 36.925 401.099 c
36.925 400.652 37.109 400.208 37.425 399.892 c
37.741 399.576 38.185 399.392 38.631 399.392 c
39.078 399.392 39.522 399.576 39.838 399.892 c
40.154 400.208 40.337 400.652 40.337 401.099 c f
BT 45.750 398.131 Td /F1 9.8 Tf  [(RAxML alpha-version 7.2.4_sse3 fast search, used for SAT�:������)] TJ ET
BT 26.250 374.976 Td /F1 9.8 Tf  [(��� raxmlHPC-SSE3� -F -D -m GTRMIX)] TJ ET
BT 26.250 355.572 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -s <input>)] TJ ET
BT 26.250 336.167 Td /F1 9.8 Tf  [(Finally, for the purposes of constructing a reference tree on the biological datasets,�other than the three largest biological )] TJ ET
BT 26.250 324.262 Td /F1 9.8 Tf  [(datasets, we used the following�command in RAxML version 7.0.4 to estimate an ML tree on the curated alignment�and assign )] TJ ET
BT 26.250 312.357 Td /F1 9.8 Tf  [(support values to the edges of the ML tree using a rapid bootstrapping�analysis with 500 bootstrap replicates:)] TJ ET
40.337 295.920 m 
40.337 296.367 40.154 296.811 39.838 297.127 c
39.522 297.443 39.078 297.626 38.631 297.626 c
38.185 297.626 37.741 297.443 37.425 297.127 c
37.109 296.811 36.925 296.367 36.925 295.920 c
36.925 295.474 37.109 295.030 37.425 294.714 c
37.741 294.398 38.185 294.214 38.631 294.214 c
39.078 294.214 39.522 294.398 39.838 294.714 c
40.154 295.030 40.337 295.474 40.337 295.920 c f
BT 45.750 292.953 Td /F1 9.8 Tf  [(RAxML rapid bootstrap:����)] TJ ET
BT 26.250 269.798 Td /F1 9.8 Tf  [(��� raxmlHPC -f a -m GTRGAMMA -s <input>)] TJ ET
BT 26.250 250.393 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -x <random number>)] TJ ET
BT 26.250 230.988 Td /F1 9.8 Tf  [(��� -p <random number> -N <number of replicates>)] TJ ET
BT 26.250 211.584 Td /F1 9.8 Tf  [(To construct a reference tree on the 16S.3 and 16S.T datasets, we first estimated�an ML tree on the curated alignment using )] TJ ET
BT 26.250 199.679 Td /F1 9.8 Tf  [(RAxML version 7.2.6 with the RAxML�default command. Then, we performed a rapid bootstrap analysis to assign support�)] TJ ET
BT 26.250 187.774 Td /F1 9.8 Tf  [(values to the edges of the ML tree using RAxML version 7.0.4 with the RAxML rapid�bootstrap command. This analysis )] TJ ET
BT 26.250 175.869 Td /F1 9.8 Tf  [(consisted of 500 rapid bootstrap replicates for�the 16S.3 dataset and 346 rapid bootstrap replicates for the 16S.T dataset.)] TJ ET
BT 26.250 156.465 Td /F1 9.8 Tf  [(To construct a reference tree on the 16S.B.ALL dataset, we first estimated�an ML tree on the curated alignment using RAxML )] TJ ET
BT 26.250 144.560 Td /F1 9.8 Tf  [(version�7.0.4 with the RAxML default command. We then assigned support values to the�edges of the ML tree using 573 )] TJ ET
BT 26.250 132.655 Td /F1 9.8 Tf  [(bootstrap replicates from two different bootstrap�analyses.�129 out of the 573 bootstrap replicates were obtained using RAxML )] TJ ET
BT 26.250 120.750 Td /F1 9.8 Tf  [(version 7.0.4�with the RAxML rapid bootstrap command listed above.�444 out of the 573 bootstrap replicates were obtained )] TJ ET
BT 26.250 108.846 Td /F1 9.8 Tf  [(using RAxML version 7.2.5�to perform a standard�bootstrap analysis on TACC's Ranger supercomputer. RAxML was run in )] TJ ET
BT 26.250 96.941 Td /F1 9.8 Tf  [(parallel on�each bootstrap replicate using the four cores of a single compute node on Ranger�via the following command:)] TJ ET
40.337 80.504 m 
40.337 80.950 40.154 81.394 39.838 81.710 c
39.522 82.026 39.078 82.210 38.631 82.210 c
38.185 82.210 37.741 82.026 37.425 81.710 c
37.109 81.394 36.925 80.950 36.925 80.504 c
36.925 80.057 37.109 79.613 37.425 79.297 c
37.741 78.981 38.185 78.797 38.631 78.797 c
39.078 78.797 39.522 78.981 39.838 79.297 c
40.154 79.613 40.337 80.057 40.337 80.504 c f
BT 45.750 77.536 Td /F1 9.8 Tf  [(RAxML analysis of a single standard bootstrap replicate:)] TJ ET
BT 26.250 54.381 Td /F1 9.8 Tf  [(���� raxmlHPC-PTHREADS-SSE3 -m GTRCAT -s <input>)] TJ ET
Q
q
15.000 44.500 577.500 732.500 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(��� prank -d=<input> -o=<output>)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(��� -t=<RAxML\(MAFFT\) guide tree> -noxml -notree)] TJ ET
BT 26.250 728.667 Td /F1 9.8 Tf  [(��� -nopost +F -matinitsize=5 -uselogs)] TJ ET
0.271 0.267 0.267 RG
40.337 712.230 m 
40.337 712.676 40.154 713.120 39.838 713.436 c
39.522 713.752 39.078 713.936 38.631 713.936 c
38.185 713.936 37.741 713.752 37.425 713.436 c
37.109 713.120 36.925 712.676 36.925 712.230 c
36.925 711.783 37.109 711.339 37.425 711.023 c
37.741 710.707 38.185 710.523 38.631 710.523 c
39.078 710.523 39.522 710.707 39.838 711.023 c
40.154 711.339 40.337 711.783 40.337 712.230 c f
BT 45.750 709.262 Td /F1 9.8 Tf  [(Opal:)] TJ ET
BT 26.250 686.107 Td /F1 9.8 Tf  [(��� java -jar Opal.1.0.2.jar --in <input>)] TJ ET
BT 26.250 666.702 Td /F1 9.8 Tf  [(��� --out <output>)] TJ ET
BT 26.250 647.298 Td /F4 9.8 Tf  [(Maximum likelihood estimation models)] TJ ET
BT 26.250 627.893 Td /F1 9.8 Tf  [(For all two-phase methods \(i.e., ML trees estimated on alignments other than in SAT�\), we computed the ML trees using either )] TJ ET
BT 26.250 615.988 Td /F1 9.8 Tf  [(RAxML version 7.0.4 or FastTree version 2.1.3, but FastTree was used only on the Price 78K dataset. All two-phase ML )] TJ ET
BT 26.250 604.083 Td /F1 9.8 Tf  [(estimations were run to completion.)] TJ ET
BT 26.250 584.679 Td /F1 9.8 Tf  [(The commands used are as follows \(<input> is a PHYLIP-formatted input alignment file\):)] TJ ET
40.337 568.241 m 
40.337 568.688 40.154 569.132 39.838 569.448 c
39.522 569.764 39.078 569.948 38.631 569.948 c
38.185 569.948 37.741 569.764 37.425 569.448 c
37.109 569.132 36.925 568.688 36.925 568.241 c
36.925 567.795 37.109 567.351 37.425 567.035 c
37.741 566.719 38.185 566.535 38.631 566.535 c
39.078 566.535 39.522 566.719 39.838 567.035 c
40.154 567.351 40.337 567.795 40.337 568.241 c f
BT 45.750 565.274 Td /F1 9.8 Tf  [(RAxML default:�������)] TJ ET
BT 26.250 542.119 Td /F1 9.8 Tf  [(��� raxmlHPC -m GTRMIX -w <work dir>)] TJ ET
BT 26.250 522.714 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -s <input>)] TJ ET
40.337 506.277 m 
40.337 506.724 40.154 507.168 39.838 507.484 c
39.522 507.800 39.078 507.983 38.631 507.983 c
38.185 507.983 37.741 507.800 37.425 507.484 c
37.109 507.168 36.925 506.724 36.925 506.277 c
36.925 505.831 37.109 505.387 37.425 505.071 c
37.741 504.755 38.185 504.571 38.631 504.571 c
39.078 504.571 39.522 504.755 39.838 505.071 c
40.154 505.387 40.337 505.831 40.337 506.277 c f
BT 45.750 503.310 Td /F1 9.8 Tf  [(FastTree:)] TJ ET
BT 26.250 480.155 Td /F1 9.8 Tf  [(��� FastTree -nt -gtr -nosupport)] TJ ET
BT 26.250 460.750 Td /F1 9.8 Tf  [(��� -log <log file> <input alignment> > <output tree>)] TJ ET
BT 26.250 441.345 Td /F1 9.8 Tf  [(�The use of RAxML within SAT� is also performed as given above, except for the three largest biological datasets. On these )] TJ ET
BT 26.250 429.441 Td /F1 9.8 Tf  [(datasets \(16S.B.ALL, 16S.T, and 16S.3\), the SAT� search utilized an alpha-version 7.2.4_sse3 of RAxML which makes use of a )] TJ ET
BT 26.250 417.536 Td /F1 9.8 Tf  [(stopping rule that permits faster runs than the default RAxML version 7.0.4 search.)] TJ ET
40.337 401.099 m 
40.337 401.545 40.154 401.989 39.838 402.305 c
39.522 402.621 39.078 402.805 38.631 402.805 c
38.185 402.805 37.741 402.621 37.425 402.305 c
37.109 401.989 36.925 401.545 36.925 401.099 c
36.925 400.652 37.109 400.208 37.425 399.892 c
37.741 399.576 38.185 399.392 38.631 399.392 c
39.078 399.392 39.522 399.576 39.838 399.892 c
40.154 400.208 40.337 400.652 40.337 401.099 c f
BT 45.750 398.131 Td /F1 9.8 Tf  [(RAxML alpha-version 7.2.4_sse3 fast search, used for SAT�:������)] TJ ET
BT 26.250 374.976 Td /F1 9.8 Tf  [(��� raxmlHPC-SSE3� -F -D -m GTRMIX)] TJ ET
BT 26.250 355.572 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -s <input>)] TJ ET
BT 26.250 336.167 Td /F1 9.8 Tf  [(Finally, for the purposes of constructing a reference tree on the biological datasets,�other than the three largest biological )] TJ ET
BT 26.250 324.262 Td /F1 9.8 Tf  [(datasets, we used the following�command in RAxML version 7.0.4 to estimate an ML tree on the curated alignment�and assign )] TJ ET
BT 26.250 312.357 Td /F1 9.8 Tf  [(support values to the edges of the ML tree using a rapid bootstrapping�analysis with 500 bootstrap replicates:)] TJ ET
40.337 295.920 m 
40.337 296.367 40.154 296.811 39.838 297.127 c
39.522 297.443 39.078 297.626 38.631 297.626 c
38.185 297.626 37.741 297.443 37.425 297.127 c
37.109 296.811 36.925 296.367 36.925 295.920 c
36.925 295.474 37.109 295.030 37.425 294.714 c
37.741 294.398 38.185 294.214 38.631 294.214 c
39.078 294.214 39.522 294.398 39.838 294.714 c
40.154 295.030 40.337 295.474 40.337 295.920 c f
BT 45.750 292.953 Td /F1 9.8 Tf  [(RAxML rapid bootstrap:����)] TJ ET
BT 26.250 269.798 Td /F1 9.8 Tf  [(��� raxmlHPC -f a -m GTRGAMMA -s <input>)] TJ ET
BT 26.250 250.393 Td /F1 9.8 Tf  [(��� -n <identifying suffix> -x <random number>)] TJ ET
BT 26.250 230.988 Td /F1 9.8 Tf  [(��� -p <random number> -N <number of replicates>)] TJ ET
BT 26.250 211.584 Td /F1 9.8 Tf  [(To construct a reference tree on the 16S.3 and 16S.T datasets, we first estimated�an ML tree on the curated alignment using )] TJ ET
BT 26.250 199.679 Td /F1 9.8 Tf  [(RAxML version 7.2.6 with the RAxML�default command. Then, we performed a rapid bootstrap analysis to assign support�)] TJ ET
BT 26.250 187.774 Td /F1 9.8 Tf  [(values to the edges of the ML tree using RAxML version 7.0.4 with the RAxML rapid�bootstrap command. This analysis )] TJ ET
BT 26.250 175.869 Td /F1 9.8 Tf  [(consisted of 500 rapid bootstrap replicates for�the 16S.3 dataset and 346 rapid bootstrap replicates for the 16S.T dataset.)] TJ ET
BT 26.250 156.465 Td /F1 9.8 Tf  [(To construct a reference tree on the 16S.B.ALL dataset, we first estimated�an ML tree on the curated alignment using RAxML )] TJ ET
BT 26.250 144.560 Td /F1 9.8 Tf  [(version�7.0.4 with the RAxML default command. We then assigned support values to the�edges of the ML tree using 573 )] TJ ET
BT 26.250 132.655 Td /F1 9.8 Tf  [(bootstrap replicates from two different bootstrap�analyses.�129 out of the 573 bootstrap replicates were obtained using RAxML )] TJ ET
BT 26.250 120.750 Td /F1 9.8 Tf  [(version 7.0.4�with the RAxML rapid bootstrap command listed above.�444 out of the 573 bootstrap replicates were obtained )] TJ ET
BT 26.250 108.846 Td /F1 9.8 Tf  [(using RAxML version 7.2.5�to perform a standard�bootstrap analysis on TACC's Ranger supercomputer. RAxML was run in )] TJ ET
BT 26.250 96.941 Td /F1 9.8 Tf  [(parallel on�each bootstrap replicate using the four cores of a single compute node on Ranger�via the following command:)] TJ ET
40.337 80.504 m 
40.337 80.950 40.154 81.394 39.838 81.710 c
39.522 82.026 39.078 82.210 38.631 82.210 c
38.185 82.210 37.741 82.026 37.425 81.710 c
37.109 81.394 36.925 80.950 36.925 80.504 c
36.925 80.057 37.109 79.613 37.425 79.297 c
37.741 78.981 38.185 78.797 38.631 78.797 c
39.078 78.797 39.522 78.981 39.838 79.297 c
40.154 79.613 40.337 80.057 40.337 80.504 c f
BT 45.750 77.536 Td /F1 9.8 Tf  [(RAxML analysis of a single standard bootstrap replicate:)] TJ ET
BT 26.250 54.381 Td /F1 9.8 Tf  [(���� raxmlHPC-PTHREADS-SSE3 -m GTRCAT -s <input>)] TJ ET
Q
q
0.000 0.000 0.000 rg
BT 291.710 19.825 Td /F1 11.0 Tf  [(9)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

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0.271 0.267 0.267 RG
q
15.000 36.039 577.500 740.961 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(���� -n <identifying suffix> -b <random number>)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(��� -p <random number> -N 1 -T 4)] TJ ET
BT 26.250 728.667 Td /F1 9.8 Tf  [(�When necessary, we enabled multithreading for the above RAxML runs either by recompiling with PTHREADS )] TJ ET
0.267 0.267 0.267 rg
BT 507.968 728.667 Td /F1 9.8 Tf  [([33])] TJ ET
0.271 0.267 0.267 rg
BT 524.231 728.667 Td /F1 9.8 Tf  [( and running )] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(with an additional flag -T <number of threads>, or by recompiling with MPI for the rapid bootstrapping analysis; this )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(parallelization does not otherwise change the RAxML commands. The RAxML outputs are unaffected by parallelization, and all )] TJ ET
BT 26.250 692.952 Td /F1 9.8 Tf  [(reported runtimes are for serialized execution.)] TJ ET
BT 26.250 673.548 Td /F4 9.8 Tf  [(SAT� estimation)] TJ ET
BT 26.250 654.143 Td /F1 9.8 Tf  [(We ran SAT� version 1.1 using the following commands:)] TJ ET
0.271 0.267 0.267 RG
40.337 637.706 m 
40.337 638.152 40.154 638.596 39.838 638.912 c
39.522 639.228 39.078 639.412 38.631 639.412 c
38.185 639.412 37.741 639.228 37.425 638.912 c
37.109 638.596 36.925 638.152 36.925 637.706 c
36.925 637.259 37.109 636.815 37.425 636.499 c
37.741 636.183 38.185 636.000 38.631 636.000 c
39.078 636.000 39.522 636.183 39.838 636.499 c
40.154 636.815 40.337 637.259 40.337 637.706 c f
BT 45.750 634.738 Td /F1 9.8 Tf  [(SAT� 24-hour search on six smallest datasets:)] TJ ET
BT 26.250 611.583 Td /F1 9.8 Tf  [(��� ./sate_basic.pl -r <name of run>)] TJ ET
BT 26.250 592.179 Td /F1 9.8 Tf  [(���� -w <empty temporary work directory with full path>)] TJ ET
BT 26.250 572.774 Td /F1 9.8 Tf  [(��� -d <input unaligned sequences file with full path>)] TJ ET
BT 26.250 553.369 Td /F1 9.8 Tf  [(��� -l 1 -s -1 -a 5)] TJ ET
40.337 536.932 m 
40.337 537.379 40.154 537.823 39.838 538.139 c
39.522 538.454 39.078 538.638 38.631 538.638 c
38.185 538.638 37.741 538.454 37.425 538.139 c
37.109 537.823 36.925 537.379 36.925 536.932 c
36.925 536.485 37.109 536.041 37.425 535.725 c
37.741 535.410 38.185 535.226 38.631 535.226 c
39.078 535.226 39.522 535.410 39.838 535.725 c
40.154 536.041 40.337 536.485 40.337 536.932 c f
BT 45.750 533.964 Td /F1 9.8 Tf  [(SAT� search for 10 iterations on four largest datasets:)] TJ ET
BT 26.250 510.810 Td /F1 9.8 Tf  [(��� ./sate_large_64.pl -r <name of run>)] TJ ET
BT 26.250 491.405 Td /F1 9.8 Tf  [(��� -w <empty temporary work directory with full path>)] TJ ET
BT 26.250 472.000 Td /F1 9.8 Tf  [(���� -d <input unaligned sequences file with full path>)] TJ ET
BT 26.250 452.595 Td /F4 9.8 Tf  [(Error calculation software)] TJ ET
BT 26.250 433.191 Td /F1 9.8 Tf  [(To compute alignment SP-FN and missing branch error rates, we used custom code, available at the Supplementary Materials )] TJ ET
BT 26.250 421.286 Td /F1 9.8 Tf  [(online webpage )] TJ ET
0.267 0.267 0.267 rg
BT 97.249 421.286 Td /F1 9.8 Tf  [([25])] TJ ET
0.271 0.267 0.267 rg
BT 113.513 421.286 Td /F1 9.8 Tf  [(.)] TJ ET
BT 26.250 401.881 Td /F4 9.8 Tf  [(Computational Resources)] TJ ET
BT 26.250 382.476 Td /F1 9.8 Tf  [(We ran the two-phase methods and SAT� on the six smaller biological datasets using a heterogeneous Condor�)] TJ ET
0.267 0.267 0.267 rg
BT 508.563 382.476 Td /F1 9.8 Tf  [([10][34])] TJ ET
0.271 0.267 0.267 rg
BT 541.089 382.476 Td /F1 9.8 Tf  [(�cluster )] TJ ET
BT 26.250 370.572 Td /F1 9.8 Tf  [(of machines. Each machine in this cluster has at least 1 core and at most 8 cores on its multi-core processor, which ran at )] TJ ET
BT 26.250 358.667 Td /F1 9.8 Tf  [(speeds between 1.86 Ghz and 3.16 Ghz. While the machines in this heterogeneous cluster are either 32-bit or 64-bit machines, )] TJ ET
BT 26.250 346.762 Td /F1 9.8 Tf  [(all machines were capable of running 32-bit executables and we only used 32-bit executables to perform these runs. Each of )] TJ ET
BT 26.250 334.857 Td /F1 9.8 Tf  [(these runs received its own dedicated core on a machine with dedicated access to at least 512 MB and at most 4 GB of main )] TJ ET
BT 26.250 322.953 Td /F1 9.8 Tf  [(memory.)] TJ ET
BT 26.250 303.548 Td /F1 9.8 Tf  [(All analyses of the four largest datasets were run using a very high-memory machine with 256 GB main memory and a 16-core )] TJ ET
BT 26.250 291.643 Td /F1 9.8 Tf  [(64-bit 2.5 Ghz AMD Opteron CPU, with the following exceptions: each of the successful runs of ML\(MAFFT-PartTree\), )] TJ ET
BT 26.250 279.738 Td /F1 9.8 Tf  [(ML\(ClustalW-quicktree\), and SAT� on the 16S.T and 16S.3 datasets and each of the failed runs of ML\(MAFFT-PartTree\) and )] TJ ET
BT 26.250 267.834 Td /F1 9.8 Tf  [(ML\(ClustalW-quicktree\) on the 16S.B.ALL dataset were performed on an individual machine with dedicated access to all 32 GB )] TJ ET
BT 26.250 255.929 Td /F1 9.8 Tf  [(of main memory and 8-core 64-bit 2.83 Ghz processors. For the runs that failed on the four largest datasets, i.e. SAT�and )] TJ ET
BT 26.250 244.024 Td /F1 9.8 Tf  [(ML\(ClustalW\) on the 16S.B.ALL dataset and ML\(MAFFT\), ML\(Prank+GT\), and ML\(Opal\) on the 16S.B.ALL and 16S.3 datasets, )] TJ ET
BT 26.250 232.119 Td /F1 9.8 Tf  [(we performed each run with dedicated access to the entire very high-memory machine and thus each run had exclusive access )] TJ ET
BT 26.250 220.215 Td /F1 9.8 Tf  [(to all 256 GB of main memory available on that machine. For the runs that succeeded or are still running on the four largest )] TJ ET
BT 26.250 208.310 Td /F1 9.8 Tf  [(datasets using the very high-memory machine, the minimum amount of memory available to each run was the total amount of )] TJ ET
BT 26.250 196.405 Td /F1 9.8 Tf  [(main memory available on the machine divided by the number of cores on the machine; however, the memory typically )] TJ ET
BT 26.250 184.500 Td /F1 9.8 Tf  [(available to each run was much closer to the total amount of main memory available on the machine.�)] TJ ET
BT 26.250 165.096 Td /F1 9.8 Tf  [(��)] TJ ET
BT 26.250 145.691 Td /F1 9.8 Tf  [(�)] TJ ET
BT 26.250 109.088 Td /F4 12.0 Tf  [(References)] TJ ET
BT 26.250 81.634 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 38.132 81.634 Td /F1 9.8 Tf  [(Cantarel BL, Morrison HG, Pearson W. Exploring the relationship between sequence similarity and accurate phylogenetic )] TJ ET
BT 26.250 69.729 Td /F1 9.8 Tf  [(trees. Mol Biol Evol. 2006 Nov;23\(11\):2090-100. Epub 2006 Aug 4. PubMed PMID: 16891377.)] TJ ET
BT 26.250 50.325 Td /F1 9.8 Tf  [(2.)] TJ ET
BT 38.132 50.325 Td /F1 9.8 Tf  [(L�ytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. )] TJ ET
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BT 26.250 716.762 Td /F1 9.8 Tf  [(with an additional flag -T <number of threads>, or by recompiling with MPI for the rapid bootstrapping analysis; this )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(parallelization does not otherwise change the RAxML commands. The RAxML outputs are unaffected by parallelization, and all )] TJ ET
BT 26.250 692.952 Td /F1 9.8 Tf  [(reported runtimes are for serialized execution.)] TJ ET
BT 26.250 673.548 Td /F4 9.8 Tf  [(SAT� estimation)] TJ ET
BT 26.250 654.143 Td /F1 9.8 Tf  [(We ran SAT� version 1.1 using the following commands:)] TJ ET
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37.109 638.596 36.925 638.152 36.925 637.706 c
36.925 637.259 37.109 636.815 37.425 636.499 c
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BT 45.750 634.738 Td /F1 9.8 Tf  [(SAT� 24-hour search on six smallest datasets:)] TJ ET
BT 26.250 611.583 Td /F1 9.8 Tf  [(��� ./sate_basic.pl -r <name of run>)] TJ ET
BT 26.250 592.179 Td /F1 9.8 Tf  [(���� -w <empty temporary work directory with full path>)] TJ ET
BT 26.250 572.774 Td /F1 9.8 Tf  [(��� -d <input unaligned sequences file with full path>)] TJ ET
BT 26.250 553.369 Td /F1 9.8 Tf  [(��� -l 1 -s -1 -a 5)] TJ ET
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BT 26.250 510.810 Td /F1 9.8 Tf  [(��� ./sate_large_64.pl -r <name of run>)] TJ ET
BT 26.250 491.405 Td /F1 9.8 Tf  [(��� -w <empty temporary work directory with full path>)] TJ ET
BT 26.250 472.000 Td /F1 9.8 Tf  [(���� -d <input unaligned sequences file with full path>)] TJ ET
BT 26.250 452.595 Td /F4 9.8 Tf  [(Error calculation software)] TJ ET
BT 26.250 433.191 Td /F1 9.8 Tf  [(To compute alignment SP-FN and missing branch error rates, we used custom code, available at the Supplementary Materials )] TJ ET
BT 26.250 421.286 Td /F1 9.8 Tf  [(online webpage )] TJ ET
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BT 26.250 370.572 Td /F1 9.8 Tf  [(of machines. Each machine in this cluster has at least 1 core and at most 8 cores on its multi-core processor, which ran at )] TJ ET
BT 26.250 358.667 Td /F1 9.8 Tf  [(speeds between 1.86 Ghz and 3.16 Ghz. While the machines in this heterogeneous cluster are either 32-bit or 64-bit machines, )] TJ ET
BT 26.250 346.762 Td /F1 9.8 Tf  [(all machines were capable of running 32-bit executables and we only used 32-bit executables to perform these runs. Each of )] TJ ET
BT 26.250 334.857 Td /F1 9.8 Tf  [(these runs received its own dedicated core on a machine with dedicated access to at least 512 MB and at most 4 GB of main )] TJ ET
BT 26.250 322.953 Td /F1 9.8 Tf  [(memory.)] TJ ET
BT 26.250 303.548 Td /F1 9.8 Tf  [(All analyses of the four largest datasets were run using a very high-memory machine with 256 GB main memory and a 16-core )] TJ ET
BT 26.250 291.643 Td /F1 9.8 Tf  [(64-bit 2.5 Ghz AMD Opteron CPU, with the following exceptions: each of the successful runs of ML\(MAFFT-PartTree\), )] TJ ET
BT 26.250 279.738 Td /F1 9.8 Tf  [(ML\(ClustalW-quicktree\), and SAT� on the 16S.T and 16S.3 datasets and each of the failed runs of ML\(MAFFT-PartTree\) and )] TJ ET
BT 26.250 267.834 Td /F1 9.8 Tf  [(ML\(ClustalW-quicktree\) on the 16S.B.ALL dataset were performed on an individual machine with dedicated access to all 32 GB )] TJ ET
BT 26.250 255.929 Td /F1 9.8 Tf  [(of main memory and 8-core 64-bit 2.83 Ghz processors. For the runs that failed on the four largest datasets, i.e. SAT�and )] TJ ET
BT 26.250 244.024 Td /F1 9.8 Tf  [(ML\(ClustalW\) on the 16S.B.ALL dataset and ML\(MAFFT\), ML\(Prank+GT\), and ML\(Opal\) on the 16S.B.ALL and 16S.3 datasets, )] TJ ET
BT 26.250 232.119 Td /F1 9.8 Tf  [(we performed each run with dedicated access to the entire very high-memory machine and thus each run had exclusive access )] TJ ET
BT 26.250 220.215 Td /F1 9.8 Tf  [(to all 256 GB of main memory available on that machine. For the runs that succeeded or are still running on the four largest )] TJ ET
BT 26.250 208.310 Td /F1 9.8 Tf  [(datasets using the very high-memory machine, the minimum amount of memory available to each run was the total amount of )] TJ ET
BT 26.250 196.405 Td /F1 9.8 Tf  [(main memory available on the machine divided by the number of cores on the machine; however, the memory typically )] TJ ET
BT 26.250 184.500 Td /F1 9.8 Tf  [(available to each run was much closer to the total amount of main memory available on the machine.�)] TJ ET
BT 26.250 165.096 Td /F1 9.8 Tf  [(��)] TJ ET
BT 26.250 145.691 Td /F1 9.8 Tf  [(�)] TJ ET
BT 26.250 109.088 Td /F4 12.0 Tf  [(References)] TJ ET
BT 26.250 81.634 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 38.132 81.634 Td /F1 9.8 Tf  [(Cantarel BL, Morrison HG, Pearson W. Exploring the relationship between sequence similarity and accurate phylogenetic )] TJ ET
BT 26.250 69.729 Td /F1 9.8 Tf  [(trees. Mol Biol Evol. 2006 Nov;23\(11\):2090-100. Epub 2006 Aug 4. PubMed PMID: 16891377.)] TJ ET
BT 26.250 50.325 Td /F1 9.8 Tf  [(2.)] TJ ET
BT 38.132 50.325 Td /F1 9.8 Tf  [(L�ytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. )] TJ ET
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BT 524.231 728.667 Td /F1 9.8 Tf  [( and running )] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(with an additional flag -T <number of threads>, or by recompiling with MPI for the rapid bootstrapping analysis; this )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(parallelization does not otherwise change the RAxML commands. The RAxML outputs are unaffected by parallelization, and all )] TJ ET
BT 26.250 692.952 Td /F1 9.8 Tf  [(reported runtimes are for serialized execution.)] TJ ET
BT 26.250 673.548 Td /F4 9.8 Tf  [(SAT� estimation)] TJ ET
BT 26.250 654.143 Td /F1 9.8 Tf  [(We ran SAT� version 1.1 using the following commands:)] TJ ET
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39.522 639.228 39.078 639.412 38.631 639.412 c
38.185 639.412 37.741 639.228 37.425 638.912 c
37.109 638.596 36.925 638.152 36.925 637.706 c
36.925 637.259 37.109 636.815 37.425 636.499 c
37.741 636.183 38.185 636.000 38.631 636.000 c
39.078 636.000 39.522 636.183 39.838 636.499 c
40.154 636.815 40.337 637.259 40.337 637.706 c f
BT 45.750 634.738 Td /F1 9.8 Tf  [(SAT� 24-hour search on six smallest datasets:)] TJ ET
BT 26.250 611.583 Td /F1 9.8 Tf  [(��� ./sate_basic.pl -r <name of run>)] TJ ET
BT 26.250 592.179 Td /F1 9.8 Tf  [(���� -w <empty temporary work directory with full path>)] TJ ET
BT 26.250 572.774 Td /F1 9.8 Tf  [(��� -d <input unaligned sequences file with full path>)] TJ ET
BT 26.250 553.369 Td /F1 9.8 Tf  [(��� -l 1 -s -1 -a 5)] TJ ET
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40.337 537.379 40.154 537.823 39.838 538.139 c
39.522 538.454 39.078 538.638 38.631 538.638 c
38.185 538.638 37.741 538.454 37.425 538.139 c
37.109 537.823 36.925 537.379 36.925 536.932 c
36.925 536.485 37.109 536.041 37.425 535.725 c
37.741 535.410 38.185 535.226 38.631 535.226 c
39.078 535.226 39.522 535.410 39.838 535.725 c
40.154 536.041 40.337 536.485 40.337 536.932 c f
BT 45.750 533.964 Td /F1 9.8 Tf  [(SAT� search for 10 iterations on four largest datasets:)] TJ ET
BT 26.250 510.810 Td /F1 9.8 Tf  [(��� ./sate_large_64.pl -r <name of run>)] TJ ET
BT 26.250 491.405 Td /F1 9.8 Tf  [(��� -w <empty temporary work directory with full path>)] TJ ET
BT 26.250 472.000 Td /F1 9.8 Tf  [(���� -d <input unaligned sequences file with full path>)] TJ ET
BT 26.250 452.595 Td /F4 9.8 Tf  [(Error calculation software)] TJ ET
BT 26.250 433.191 Td /F1 9.8 Tf  [(To compute alignment SP-FN and missing branch error rates, we used custom code, available at the Supplementary Materials )] TJ ET
BT 26.250 421.286 Td /F1 9.8 Tf  [(online webpage )] TJ ET
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BT 508.563 382.476 Td /F1 9.8 Tf  [([10][34])] TJ ET
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BT 26.250 255.929 Td /F1 9.8 Tf  [(of main memory and 8-core 64-bit 2.83 Ghz processors. For the runs that failed on the four largest datasets, i.e. SAT�and )] TJ ET
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BT 26.250 232.119 Td /F1 9.8 Tf  [(we performed each run with dedicated access to the entire very high-memory machine and thus each run had exclusive access )] TJ ET
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BT 26.250 196.405 Td /F1 9.8 Tf  [(main memory available on the machine divided by the number of cores on the machine; however, the memory typically )] TJ ET
BT 26.250 184.500 Td /F1 9.8 Tf  [(available to each run was much closer to the total amount of main memory available on the machine.�)] TJ ET
BT 26.250 165.096 Td /F1 9.8 Tf  [(��)] TJ ET
BT 26.250 145.691 Td /F1 9.8 Tf  [(�)] TJ ET
BT 26.250 109.088 Td /F4 12.0 Tf  [(References)] TJ ET
BT 26.250 81.634 Td /F1 9.8 Tf  [(1.)] TJ ET
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BT 26.250 69.729 Td /F1 9.8 Tf  [(trees. Mol Biol Evol. 2006 Nov;23\(11\):2090-100. Epub 2006 Aug 4. PubMed PMID: 16891377.)] TJ ET
BT 26.250 50.325 Td /F1 9.8 Tf  [(2.)] TJ ET
BT 38.132 50.325 Td /F1 9.8 Tf  [(L�ytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. )] TJ ET
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BT 26.250 767.476 Td /F1 9.8 Tf  [(Science. 2008 Jun 20;320\(5883\):1632-5. PubMed PMID: 18566285.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(3.)] TJ ET
BT 38.132 748.071 Td /F1 9.8 Tf  [(Hall BG. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol Biol Evol. )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(2005 Mar;22\(3\):792-802. Epub 2004 Dec 8. Erratum in: Mol Biol Evol. 2005 Apr;22\(4\):1160. PubMed PMID: 15590907.)] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(4.)] TJ ET
BT 38.132 716.762 Td /F1 9.8 Tf  [(Morrison DA, Ellis JT. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(apicomplexa. Mol Biol Evol. 1997 Apr;14\(4\):428-41. PubMed PMID: 9100373.)] TJ ET
BT 26.250 685.452 Td /F1 9.8 Tf  [(5.)] TJ ET
BT 38.132 685.452 Td /F1 9.8 Tf  [(Ogden TH, Rosenberg MS. Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol. 2006 Apr;55\(2\):314-)] TJ ET
BT 26.250 673.548 Td /F1 9.8 Tf  [(28. PubMed PMID: 16611602.)] TJ ET
BT 26.250 654.143 Td /F1 9.8 Tf  [(6.)] TJ ET
BT 38.132 654.143 Td /F1 9.8 Tf  [(Roshan U, Livesay DR, Chikkagoudar S. Improving progressive alignment for phylogeny reconstruction using parsimonious )] TJ ET
BT 26.250 642.238 Td /F1 9.8 Tf  [(guide-trees. In Proceedings of the IEEE 6th Symposium on Bioinformatics and Bioengineering. IEEE Computer Society Press, )] TJ ET
BT 26.250 630.333 Td /F1 9.8 Tf  [(2006.)] TJ ET
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BT 38.132 610.929 Td /F1 9.8 Tf  [(Wang L, Leebens-Mack J, Wall P, Beckmann K, dePamphilis C, Warnow T. The impact of multiple protein sequence )] TJ ET
BT 26.250 599.024 Td /F1 9.8 Tf  [(alignment on phylogenetic estimation. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2009; PP\(99\):1 )] TJ ET
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BT 26.250 567.714 Td /F1 9.8 Tf  [(8.)] TJ ET
BT 38.132 567.714 Td /F1 9.8 Tf  [(Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment )] TJ ET
BT 26.250 555.810 Td /F1 9.8 Tf  [(through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov )] TJ ET
BT 26.250 543.905 Td /F1 9.8 Tf  [(11;22\(22\):4673-80. PubMed PMID: 7984417; PubMed Central PMCID: PMC308517.)] TJ ET
BT 26.250 524.500 Td /F1 9.8 Tf  [(9.)] TJ ET
BT 38.132 524.500 Td /F1 9.8 Tf  [(Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008 )] TJ ET
BT 26.250 512.595 Td /F1 9.8 Tf  [(Jul;9\(4\):286-98. Epub 2008 Mar 27. PubMed PMID: 18372315.)] TJ ET
BT 26.250 493.191 Td /F1 9.8 Tf  [(10.)] TJ ET
BT 43.553 493.191 Td /F1 9.8 Tf  [(Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol )] TJ ET
BT 26.250 481.286 Td /F1 9.8 Tf  [(Biol. 2000 Sep 8;302\(1\):205-17. PubMed PMID: 10964570.)] TJ ET
BT 26.250 461.881 Td /F1 9.8 Tf  [(11.)] TJ ET
BT 43.553 461.881 Td /F1 9.8 Tf  [(Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence )] TJ ET
BT 26.250 449.976 Td /F1 9.8 Tf  [(alignment. Genome Res. 2005 Feb;15\(2\):330-40. PubMed PMID: 15687296; PubMed Central PMCID: PMC546535.)] TJ ET
BT 26.250 430.572 Td /F1 9.8 Tf  [(12.)] TJ ET
BT 43.553 430.572 Td /F1 9.8 Tf  [(Var�n A, Vinh LS, Wheeler WC. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics. 2010:26.)] TJ ET
BT 26.250 411.167 Td /F1 9.8 Tf  [(13.)] TJ ET
BT 43.553 411.167 Td /F1 9.8 Tf  [(Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. )] TJ ET
BT 26.250 399.262 Td /F1 9.8 Tf  [(2004 Aug 19;5:113. PubMed PMID: 15318951; PubMed Central PMCID: PMC517706.)] TJ ET
BT 26.250 379.857 Td /F1 9.8 Tf  [(14.)] TJ ET
BT 43.553 379.857 Td /F1 9.8 Tf  [(Wheeler TJ, Kececioglu JD. Multiple alignment by aligning alignments. Bioinformatics. 2007 Jul 1;23\(13\):i559-68. PubMed )] TJ ET
BT 26.250 367.953 Td /F1 9.8 Tf  [(PMID: 17646343.)] TJ ET
BT 26.250 348.548 Td /F1 9.8 Tf  [(15.)] TJ ET
BT 43.553 348.548 Td /F1 9.8 Tf  [(L�ytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci )] TJ ET
BT 26.250 336.643 Td /F1 9.8 Tf  [(U S A. 2005 Jul 26;102\(30\):10557-62. Epub 2005 Jul 6. PubMed PMID: 16000407; PubMed Central PMCID: PMC1180752.)] TJ ET
BT 26.250 317.238 Td /F1 9.8 Tf  [(16.)] TJ ET
BT 43.553 317.238 Td /F1 9.8 Tf  [(Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T. Rapid and accurate large-scale coestimation of sequence alignments )] TJ ET
BT 26.250 305.334 Td /F1 9.8 Tf  [(and phylogenetic trees. Science. 2009 Jun 19;324\(5934\):1561-4. PubMed PMID: 19541996.)] TJ ET
BT 26.250 285.929 Td /F1 9.8 Tf  [(17.)] TJ ET
BT 43.553 285.929 Td /F1 9.8 Tf  [(Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. PLoS Comput )] TJ ET
BT 26.250 274.024 Td /F1 9.8 Tf  [(Biol. 2009 May;5\(5\):e1000392. Epub 2009 May 29. PubMed PMID: 19478997; PubMed Central PMCID: PMC2684580.)] TJ ET
BT 26.250 254.619 Td /F1 9.8 Tf  [(18.)] TJ ET
BT 43.553 254.619 Td /F1 9.8 Tf  [(Liu K, Nelesen S, Raghavan S, Linder CR, Warnow T. Barking up the wrong treelength: the impact of gap penalty on )] TJ ET
BT 26.250 242.715 Td /F1 9.8 Tf  [(alignment and tree accuracy. IEEE Transactions on Computational Biology and Bioinformatics. 2009; 6\(1\):7�21. PubMed PMID: )] TJ ET
BT 26.250 230.810 Td /F1 9.8 Tf  [(19179695.)] TJ ET
BT 26.250 211.405 Td /F1 9.8 Tf  [(19.)] TJ ET
BT 43.553 211.405 Td /F1 9.8 Tf  [(Edgar RC, Sj�lander K. SATCHMO: sequence alignment and tree construction using hidden Markov models. )] TJ ET
BT 26.250 199.500 Td /F1 9.8 Tf  [(Bioinformatics. 2003 Jul 22;19\(11\):1404-11. PubMed PMID: 12874053.)] TJ ET
BT 26.250 180.096 Td /F1 9.8 Tf  [(20.)] TJ ET
BT 43.553 180.096 Td /F1 9.8 Tf  [(Roshan U, Livesay DR. Probalign: multiple sequence alignment using partition function posterior probabilities. )] TJ ET
BT 26.250 168.191 Td /F1 9.8 Tf  [(Bioinformatics. 2006 Nov 15;22\(22\):2715-21. Epub 2006 Sep 5. PubMed PMID: 16954142.)] TJ ET
BT 26.250 148.786 Td /F1 9.8 Tf  [(21.)] TJ ET
BT 43.553 148.786 Td /F1 9.8 Tf  [(Nelesen S, Liu K, Zhao D, Linder CR, Warnow T. The effect of the guide tree on multiple sequence alignments and )] TJ ET
BT 26.250 136.881 Td /F1 9.8 Tf  [(subsequent phylogenetic analyses. Pac Symp Biocomput. 2008:25-36. PubMed PMID: 18229674.)] TJ ET
BT 26.250 117.477 Td /F1 9.8 Tf  [(22.)] TJ ET
BT 43.553 117.477 Td /F1 9.8 Tf  [(Redelings, B, Suchard M.A. Joint Bayesian estimation of alignment and phylogeny, Systematic Biology 54\(3\):401-418, )] TJ ET
BT 26.250 105.572 Td /F1 9.8 Tf  [(2005.)] TJ ET
BT 26.250 86.167 Td /F1 9.8 Tf  [(23.)] TJ ET
BT 43.553 86.167 Td /F1 9.8 Tf  [(Stamatakis A. Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective. In Proc. of )] TJ ET
BT 26.250 74.262 Td /F1 9.8 Tf  [(IPDPS2006, HICOMB Workshop, Proceedings on CD, Rhodos, Greece, April 2006.)] TJ ET
BT 26.250 54.858 Td /F1 9.8 Tf  [(24.)] TJ ET
BT 43.553 54.858 Td /F1 9.8 Tf  [(Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. )] TJ ET
Q
q
15.000 40.572 577.500 736.428 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(Science. 2008 Jun 20;320\(5883\):1632-5. PubMed PMID: 18566285.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(3.)] TJ ET
BT 38.132 748.071 Td /F1 9.8 Tf  [(Hall BG. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol Biol Evol. )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(2005 Mar;22\(3\):792-802. Epub 2004 Dec 8. Erratum in: Mol Biol Evol. 2005 Apr;22\(4\):1160. PubMed PMID: 15590907.)] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(4.)] TJ ET
BT 38.132 716.762 Td /F1 9.8 Tf  [(Morrison DA, Ellis JT. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(apicomplexa. Mol Biol Evol. 1997 Apr;14\(4\):428-41. PubMed PMID: 9100373.)] TJ ET
BT 26.250 685.452 Td /F1 9.8 Tf  [(5.)] TJ ET
BT 38.132 685.452 Td /F1 9.8 Tf  [(Ogden TH, Rosenberg MS. Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol. 2006 Apr;55\(2\):314-)] TJ ET
BT 26.250 673.548 Td /F1 9.8 Tf  [(28. PubMed PMID: 16611602.)] TJ ET
BT 26.250 654.143 Td /F1 9.8 Tf  [(6.)] TJ ET
BT 38.132 654.143 Td /F1 9.8 Tf  [(Roshan U, Livesay DR, Chikkagoudar S. Improving progressive alignment for phylogeny reconstruction using parsimonious )] TJ ET
BT 26.250 642.238 Td /F1 9.8 Tf  [(guide-trees. In Proceedings of the IEEE 6th Symposium on Bioinformatics and Bioengineering. IEEE Computer Society Press, )] TJ ET
BT 26.250 630.333 Td /F1 9.8 Tf  [(2006.)] TJ ET
BT 26.250 610.929 Td /F1 9.8 Tf  [(7.)] TJ ET
BT 38.132 610.929 Td /F1 9.8 Tf  [(Wang L, Leebens-Mack J, Wall P, Beckmann K, dePamphilis C, Warnow T. The impact of multiple protein sequence )] TJ ET
BT 26.250 599.024 Td /F1 9.8 Tf  [(alignment on phylogenetic estimation. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2009; PP\(99\):1 )] TJ ET
BT 26.250 587.119 Td /F1 9.8 Tf  [(�1.)] TJ ET
BT 26.250 567.714 Td /F1 9.8 Tf  [(8.)] TJ ET
BT 38.132 567.714 Td /F1 9.8 Tf  [(Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment )] TJ ET
BT 26.250 555.810 Td /F1 9.8 Tf  [(through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov )] TJ ET
BT 26.250 543.905 Td /F1 9.8 Tf  [(11;22\(22\):4673-80. PubMed PMID: 7984417; PubMed Central PMCID: PMC308517.)] TJ ET
BT 26.250 524.500 Td /F1 9.8 Tf  [(9.)] TJ ET
BT 38.132 524.500 Td /F1 9.8 Tf  [(Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008 )] TJ ET
BT 26.250 512.595 Td /F1 9.8 Tf  [(Jul;9\(4\):286-98. Epub 2008 Mar 27. PubMed PMID: 18372315.)] TJ ET
BT 26.250 493.191 Td /F1 9.8 Tf  [(10.)] TJ ET
BT 43.553 493.191 Td /F1 9.8 Tf  [(Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol )] TJ ET
BT 26.250 481.286 Td /F1 9.8 Tf  [(Biol. 2000 Sep 8;302\(1\):205-17. PubMed PMID: 10964570.)] TJ ET
BT 26.250 461.881 Td /F1 9.8 Tf  [(11.)] TJ ET
BT 43.553 461.881 Td /F1 9.8 Tf  [(Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence )] TJ ET
BT 26.250 449.976 Td /F1 9.8 Tf  [(alignment. Genome Res. 2005 Feb;15\(2\):330-40. PubMed PMID: 15687296; PubMed Central PMCID: PMC546535.)] TJ ET
BT 26.250 430.572 Td /F1 9.8 Tf  [(12.)] TJ ET
BT 43.553 430.572 Td /F1 9.8 Tf  [(Var�n A, Vinh LS, Wheeler WC. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics. 2010:26.)] TJ ET
BT 26.250 411.167 Td /F1 9.8 Tf  [(13.)] TJ ET
BT 43.553 411.167 Td /F1 9.8 Tf  [(Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. )] TJ ET
BT 26.250 399.262 Td /F1 9.8 Tf  [(2004 Aug 19;5:113. PubMed PMID: 15318951; PubMed Central PMCID: PMC517706.)] TJ ET
BT 26.250 379.857 Td /F1 9.8 Tf  [(14.)] TJ ET
BT 43.553 379.857 Td /F1 9.8 Tf  [(Wheeler TJ, Kececioglu JD. Multiple alignment by aligning alignments. Bioinformatics. 2007 Jul 1;23\(13\):i559-68. PubMed )] TJ ET
BT 26.250 367.953 Td /F1 9.8 Tf  [(PMID: 17646343.)] TJ ET
BT 26.250 348.548 Td /F1 9.8 Tf  [(15.)] TJ ET
BT 43.553 348.548 Td /F1 9.8 Tf  [(L�ytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci )] TJ ET
BT 26.250 336.643 Td /F1 9.8 Tf  [(U S A. 2005 Jul 26;102\(30\):10557-62. Epub 2005 Jul 6. PubMed PMID: 16000407; PubMed Central PMCID: PMC1180752.)] TJ ET
BT 26.250 317.238 Td /F1 9.8 Tf  [(16.)] TJ ET
BT 43.553 317.238 Td /F1 9.8 Tf  [(Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T. Rapid and accurate large-scale coestimation of sequence alignments )] TJ ET
BT 26.250 305.334 Td /F1 9.8 Tf  [(and phylogenetic trees. Science. 2009 Jun 19;324\(5934\):1561-4. PubMed PMID: 19541996.)] TJ ET
BT 26.250 285.929 Td /F1 9.8 Tf  [(17.)] TJ ET
BT 43.553 285.929 Td /F1 9.8 Tf  [(Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. PLoS Comput )] TJ ET
BT 26.250 274.024 Td /F1 9.8 Tf  [(Biol. 2009 May;5\(5\):e1000392. Epub 2009 May 29. PubMed PMID: 19478997; PubMed Central PMCID: PMC2684580.)] TJ ET
BT 26.250 254.619 Td /F1 9.8 Tf  [(18.)] TJ ET
BT 43.553 254.619 Td /F1 9.8 Tf  [(Liu K, Nelesen S, Raghavan S, Linder CR, Warnow T. Barking up the wrong treelength: the impact of gap penalty on )] TJ ET
BT 26.250 242.715 Td /F1 9.8 Tf  [(alignment and tree accuracy. IEEE Transactions on Computational Biology and Bioinformatics. 2009; 6\(1\):7�21. PubMed PMID: )] TJ ET
BT 26.250 230.810 Td /F1 9.8 Tf  [(19179695.)] TJ ET
BT 26.250 211.405 Td /F1 9.8 Tf  [(19.)] TJ ET
BT 43.553 211.405 Td /F1 9.8 Tf  [(Edgar RC, Sj�lander K. SATCHMO: sequence alignment and tree construction using hidden Markov models. )] TJ ET
BT 26.250 199.500 Td /F1 9.8 Tf  [(Bioinformatics. 2003 Jul 22;19\(11\):1404-11. PubMed PMID: 12874053.)] TJ ET
BT 26.250 180.096 Td /F1 9.8 Tf  [(20.)] TJ ET
BT 43.553 180.096 Td /F1 9.8 Tf  [(Roshan U, Livesay DR. Probalign: multiple sequence alignment using partition function posterior probabilities. )] TJ ET
BT 26.250 168.191 Td /F1 9.8 Tf  [(Bioinformatics. 2006 Nov 15;22\(22\):2715-21. Epub 2006 Sep 5. PubMed PMID: 16954142.)] TJ ET
BT 26.250 148.786 Td /F1 9.8 Tf  [(21.)] TJ ET
BT 43.553 148.786 Td /F1 9.8 Tf  [(Nelesen S, Liu K, Zhao D, Linder CR, Warnow T. The effect of the guide tree on multiple sequence alignments and )] TJ ET
BT 26.250 136.881 Td /F1 9.8 Tf  [(subsequent phylogenetic analyses. Pac Symp Biocomput. 2008:25-36. PubMed PMID: 18229674.)] TJ ET
BT 26.250 117.477 Td /F1 9.8 Tf  [(22.)] TJ ET
BT 43.553 117.477 Td /F1 9.8 Tf  [(Redelings, B, Suchard M.A. Joint Bayesian estimation of alignment and phylogeny, Systematic Biology 54\(3\):401-418, )] TJ ET
BT 26.250 105.572 Td /F1 9.8 Tf  [(2005.)] TJ ET
BT 26.250 86.167 Td /F1 9.8 Tf  [(23.)] TJ ET
BT 43.553 86.167 Td /F1 9.8 Tf  [(Stamatakis A. Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective. In Proc. of )] TJ ET
BT 26.250 74.262 Td /F1 9.8 Tf  [(IPDPS2006, HICOMB Workshop, Proceedings on CD, Rhodos, Greece, April 2006.)] TJ ET
BT 26.250 54.858 Td /F1 9.8 Tf  [(24.)] TJ ET
BT 43.553 54.858 Td /F1 9.8 Tf  [(Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. )] TJ ET
Q
q
15.000 40.572 577.500 736.428 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(Science. 2008 Jun 20;320\(5883\):1632-5. PubMed PMID: 18566285.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(3.)] TJ ET
BT 38.132 748.071 Td /F1 9.8 Tf  [(Hall BG. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol Biol Evol. )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(2005 Mar;22\(3\):792-802. Epub 2004 Dec 8. Erratum in: Mol Biol Evol. 2005 Apr;22\(4\):1160. PubMed PMID: 15590907.)] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(4.)] TJ ET
BT 38.132 716.762 Td /F1 9.8 Tf  [(Morrison DA, Ellis JT. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(apicomplexa. Mol Biol Evol. 1997 Apr;14\(4\):428-41. PubMed PMID: 9100373.)] TJ ET
BT 26.250 685.452 Td /F1 9.8 Tf  [(5.)] TJ ET
BT 38.132 685.452 Td /F1 9.8 Tf  [(Ogden TH, Rosenberg MS. Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol. 2006 Apr;55\(2\):314-)] TJ ET
BT 26.250 673.548 Td /F1 9.8 Tf  [(28. PubMed PMID: 16611602.)] TJ ET
BT 26.250 654.143 Td /F1 9.8 Tf  [(6.)] TJ ET
BT 38.132 654.143 Td /F1 9.8 Tf  [(Roshan U, Livesay DR, Chikkagoudar S. Improving progressive alignment for phylogeny reconstruction using parsimonious )] TJ ET
BT 26.250 642.238 Td /F1 9.8 Tf  [(guide-trees. In Proceedings of the IEEE 6th Symposium on Bioinformatics and Bioengineering. IEEE Computer Society Press, )] TJ ET
BT 26.250 630.333 Td /F1 9.8 Tf  [(2006.)] TJ ET
BT 26.250 610.929 Td /F1 9.8 Tf  [(7.)] TJ ET
BT 38.132 610.929 Td /F1 9.8 Tf  [(Wang L, Leebens-Mack J, Wall P, Beckmann K, dePamphilis C, Warnow T. The impact of multiple protein sequence )] TJ ET
BT 26.250 599.024 Td /F1 9.8 Tf  [(alignment on phylogenetic estimation. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2009; PP\(99\):1 )] TJ ET
BT 26.250 587.119 Td /F1 9.8 Tf  [(�1.)] TJ ET
BT 26.250 567.714 Td /F1 9.8 Tf  [(8.)] TJ ET
BT 38.132 567.714 Td /F1 9.8 Tf  [(Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment )] TJ ET
BT 26.250 555.810 Td /F1 9.8 Tf  [(through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov )] TJ ET
BT 26.250 543.905 Td /F1 9.8 Tf  [(11;22\(22\):4673-80. PubMed PMID: 7984417; PubMed Central PMCID: PMC308517.)] TJ ET
BT 26.250 524.500 Td /F1 9.8 Tf  [(9.)] TJ ET
BT 38.132 524.500 Td /F1 9.8 Tf  [(Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008 )] TJ ET
BT 26.250 512.595 Td /F1 9.8 Tf  [(Jul;9\(4\):286-98. Epub 2008 Mar 27. PubMed PMID: 18372315.)] TJ ET
BT 26.250 493.191 Td /F1 9.8 Tf  [(10.)] TJ ET
BT 43.553 493.191 Td /F1 9.8 Tf  [(Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol )] TJ ET
BT 26.250 481.286 Td /F1 9.8 Tf  [(Biol. 2000 Sep 8;302\(1\):205-17. PubMed PMID: 10964570.)] TJ ET
BT 26.250 461.881 Td /F1 9.8 Tf  [(11.)] TJ ET
BT 43.553 461.881 Td /F1 9.8 Tf  [(Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence )] TJ ET
BT 26.250 449.976 Td /F1 9.8 Tf  [(alignment. Genome Res. 2005 Feb;15\(2\):330-40. PubMed PMID: 15687296; PubMed Central PMCID: PMC546535.)] TJ ET
BT 26.250 430.572 Td /F1 9.8 Tf  [(12.)] TJ ET
BT 43.553 430.572 Td /F1 9.8 Tf  [(Var�n A, Vinh LS, Wheeler WC. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics. 2010:26.)] TJ ET
BT 26.250 411.167 Td /F1 9.8 Tf  [(13.)] TJ ET
BT 43.553 411.167 Td /F1 9.8 Tf  [(Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. )] TJ ET
BT 26.250 399.262 Td /F1 9.8 Tf  [(2004 Aug 19;5:113. PubMed PMID: 15318951; PubMed Central PMCID: PMC517706.)] TJ ET
BT 26.250 379.857 Td /F1 9.8 Tf  [(14.)] TJ ET
BT 43.553 379.857 Td /F1 9.8 Tf  [(Wheeler TJ, Kececioglu JD. Multiple alignment by aligning alignments. Bioinformatics. 2007 Jul 1;23\(13\):i559-68. PubMed )] TJ ET
BT 26.250 367.953 Td /F1 9.8 Tf  [(PMID: 17646343.)] TJ ET
BT 26.250 348.548 Td /F1 9.8 Tf  [(15.)] TJ ET
BT 43.553 348.548 Td /F1 9.8 Tf  [(L�ytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci )] TJ ET
BT 26.250 336.643 Td /F1 9.8 Tf  [(U S A. 2005 Jul 26;102\(30\):10557-62. Epub 2005 Jul 6. PubMed PMID: 16000407; PubMed Central PMCID: PMC1180752.)] TJ ET
BT 26.250 317.238 Td /F1 9.8 Tf  [(16.)] TJ ET
BT 43.553 317.238 Td /F1 9.8 Tf  [(Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T. Rapid and accurate large-scale coestimation of sequence alignments )] TJ ET
BT 26.250 305.334 Td /F1 9.8 Tf  [(and phylogenetic trees. Science. 2009 Jun 19;324\(5934\):1561-4. PubMed PMID: 19541996.)] TJ ET
BT 26.250 285.929 Td /F1 9.8 Tf  [(17.)] TJ ET
BT 43.553 285.929 Td /F1 9.8 Tf  [(Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. PLoS Comput )] TJ ET
BT 26.250 274.024 Td /F1 9.8 Tf  [(Biol. 2009 May;5\(5\):e1000392. Epub 2009 May 29. PubMed PMID: 19478997; PubMed Central PMCID: PMC2684580.)] TJ ET
BT 26.250 254.619 Td /F1 9.8 Tf  [(18.)] TJ ET
BT 43.553 254.619 Td /F1 9.8 Tf  [(Liu K, Nelesen S, Raghavan S, Linder CR, Warnow T. Barking up the wrong treelength: the impact of gap penalty on )] TJ ET
BT 26.250 242.715 Td /F1 9.8 Tf  [(alignment and tree accuracy. IEEE Transactions on Computational Biology and Bioinformatics. 2009; 6\(1\):7�21. PubMed PMID: )] TJ ET
BT 26.250 230.810 Td /F1 9.8 Tf  [(19179695.)] TJ ET
BT 26.250 211.405 Td /F1 9.8 Tf  [(19.)] TJ ET
BT 43.553 211.405 Td /F1 9.8 Tf  [(Edgar RC, Sj�lander K. SATCHMO: sequence alignment and tree construction using hidden Markov models. )] TJ ET
BT 26.250 199.500 Td /F1 9.8 Tf  [(Bioinformatics. 2003 Jul 22;19\(11\):1404-11. PubMed PMID: 12874053.)] TJ ET
BT 26.250 180.096 Td /F1 9.8 Tf  [(20.)] TJ ET
BT 43.553 180.096 Td /F1 9.8 Tf  [(Roshan U, Livesay DR. Probalign: multiple sequence alignment using partition function posterior probabilities. )] TJ ET
BT 26.250 168.191 Td /F1 9.8 Tf  [(Bioinformatics. 2006 Nov 15;22\(22\):2715-21. Epub 2006 Sep 5. PubMed PMID: 16954142.)] TJ ET
BT 26.250 148.786 Td /F1 9.8 Tf  [(21.)] TJ ET
BT 43.553 148.786 Td /F1 9.8 Tf  [(Nelesen S, Liu K, Zhao D, Linder CR, Warnow T. The effect of the guide tree on multiple sequence alignments and )] TJ ET
BT 26.250 136.881 Td /F1 9.8 Tf  [(subsequent phylogenetic analyses. Pac Symp Biocomput. 2008:25-36. PubMed PMID: 18229674.)] TJ ET
BT 26.250 117.477 Td /F1 9.8 Tf  [(22.)] TJ ET
BT 43.553 117.477 Td /F1 9.8 Tf  [(Redelings, B, Suchard M.A. Joint Bayesian estimation of alignment and phylogeny, Systematic Biology 54\(3\):401-418, )] TJ ET
BT 26.250 105.572 Td /F1 9.8 Tf  [(2005.)] TJ ET
BT 26.250 86.167 Td /F1 9.8 Tf  [(23.)] TJ ET
BT 43.553 86.167 Td /F1 9.8 Tf  [(Stamatakis A. Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective. In Proc. of )] TJ ET
BT 26.250 74.262 Td /F1 9.8 Tf  [(IPDPS2006, HICOMB Workshop, Proceedings on CD, Rhodos, Greece, April 2006.)] TJ ET
BT 26.250 54.858 Td /F1 9.8 Tf  [(24.)] TJ ET
BT 43.553 54.858 Td /F1 9.8 Tf  [(Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. )] TJ ET
Q
q
0.000 0.000 0.000 rg
BT 291.710 19.825 Td /F1 11.0 Tf  [(11)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

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BT 26.250 767.476 Td /F1 9.8 Tf  [(Bioinformatics. 2006 Nov 1;22\(21\):2688-90. Epub 2006 Aug 23. PubMed PMID: 16928733.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(25.)] TJ ET
BT 43.553 748.071 Td /F1 9.8 Tf  [(Liu K, Linder CR, Warnow T. Supplementary online materials for PLoS Currents. Website, 2010. Available at )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(http://www.cs.utexas.edu/~phylo/datasets/tol/tol.html.)] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(26.)] TJ ET
BT 43.553 716.762 Td /F1 9.8 Tf  [(Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(matrix. Mol Biol Evol. 2009 Jul;26\(7\):1641-50. Epub 2009 Apr 17. PubMed PMID: 19377059; PubMed Central PMCID: )] TJ ET
BT 26.250 692.952 Td /F1 9.8 Tf  [(PMC2693737.)] TJ ET
BT 26.250 673.548 Td /F1 9.8 Tf  [(27.)] TJ ET
BT 43.553 673.548 Td /F1 9.8 Tf  [(Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010 )] TJ ET
BT 26.250 661.643 Td /F1 9.8 Tf  [(Mar 10;5\(3\):e9490. PubMed PMID: 20224823; PubMed Central PMCID: PMC2835736.)] TJ ET
BT 26.250 642.238 Td /F1 9.8 Tf  [(28.)] TJ ET
BT 43.553 642.238 Td /F1 9.8 Tf  [(Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, M�ller KM, Pande )] TJ ET
BT 26.250 630.333 Td /F1 9.8 Tf  [(N, Shang Z, Yu N, Gutell RR. The comparative RNA web \(CRW\) site: an online database of comparative sequence and )] TJ ET
BT 26.250 618.429 Td /F1 9.8 Tf  [(structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2. Epub 2002 Jan 17. Erratum in: BMC )] TJ ET
BT 26.250 606.524 Td /F1 9.8 Tf  [(Bioinformatics. 2002 Jul;3\(1\):15. PubMed PMID: 11869452; PubMed Central PMCID: PMC65690.)] TJ ET
BT 26.250 587.119 Td /F1 9.8 Tf  [(29.)] TJ ET
BT 43.553 587.119 Td /F1 9.8 Tf  [(Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008 )] TJ ET
BT 26.250 575.214 Td /F1 9.8 Tf  [(Oct;57\(5\):758-71. PubMed PMID: 18853362.)] TJ ET
BT 26.250 555.810 Td /F1 9.8 Tf  [(30.)] TJ ET
BT 43.553 555.810 Td /F1 9.8 Tf  [(Katoh K, Toh H. PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. )] TJ ET
BT 26.250 543.905 Td /F1 9.8 Tf  [(Bioinformatics. 2007 Feb 1;23\(3\):372-4. Epub 2006 Nov 21. PubMed PMID: 17118958.)] TJ ET
BT 26.250 524.500 Td /F1 9.8 Tf  [(31.)] TJ ET
BT 43.553 524.500 Td /F1 9.8 Tf  [(Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids )] TJ ET
BT 26.250 512.595 Td /F1 9.8 Tf  [(Res. 1999 Jul 1;27\(13\):2682-90. PubMed PMID: 10373585; PubMed Central PMCID: PMC148477.)] TJ ET
BT 26.250 493.191 Td /F1 9.8 Tf  [(32.)] TJ ET
BT 43.553 493.191 Td /F1 9.8 Tf  [(Robinson DF, Foulds LR. Comparison of phylogenetic trees. Mathematical Biosciences. 1981; 53:131�147.)] TJ ET
BT 26.250 473.786 Td /F1 9.8 Tf  [(33.)] TJ ET
BT 43.553 473.786 Td /F1 9.8 Tf  [(Ott M, Zola J, Aluru S, Stamatakis A. Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. )] TJ ET
BT 26.250 461.881 Td /F1 9.8 Tf  [(Proceedings of ACM/IEEE Supercomputing Conference 2007. 2007.)] TJ ET
BT 26.250 442.476 Td /F1 9.8 Tf  [(34.)] TJ ET
BT 43.553 442.476 Td /F1 9.8 Tf  [(Litzkow M. Remote Unix - turning idle workstations into cycle servers. In Usenix Summer Conference, pages 381�384, )] TJ ET
BT 26.250 430.572 Td /F1 9.8 Tf  [(1987.)] TJ ET
Q
q
15.000 413.191 577.500 363.809 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(Bioinformatics. 2006 Nov 1;22\(21\):2688-90. Epub 2006 Aug 23. PubMed PMID: 16928733.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(25.)] TJ ET
BT 43.553 748.071 Td /F1 9.8 Tf  [(Liu K, Linder CR, Warnow T. Supplementary online materials for PLoS Currents. Website, 2010. Available at )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(http://www.cs.utexas.edu/~phylo/datasets/tol/tol.html.)] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(26.)] TJ ET
BT 43.553 716.762 Td /F1 9.8 Tf  [(Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(matrix. Mol Biol Evol. 2009 Jul;26\(7\):1641-50. Epub 2009 Apr 17. PubMed PMID: 19377059; PubMed Central PMCID: )] TJ ET
BT 26.250 692.952 Td /F1 9.8 Tf  [(PMC2693737.)] TJ ET
BT 26.250 673.548 Td /F1 9.8 Tf  [(27.)] TJ ET
BT 43.553 673.548 Td /F1 9.8 Tf  [(Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010 )] TJ ET
BT 26.250 661.643 Td /F1 9.8 Tf  [(Mar 10;5\(3\):e9490. PubMed PMID: 20224823; PubMed Central PMCID: PMC2835736.)] TJ ET
BT 26.250 642.238 Td /F1 9.8 Tf  [(28.)] TJ ET
BT 43.553 642.238 Td /F1 9.8 Tf  [(Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, M�ller KM, Pande )] TJ ET
BT 26.250 630.333 Td /F1 9.8 Tf  [(N, Shang Z, Yu N, Gutell RR. The comparative RNA web \(CRW\) site: an online database of comparative sequence and )] TJ ET
BT 26.250 618.429 Td /F1 9.8 Tf  [(structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2. Epub 2002 Jan 17. Erratum in: BMC )] TJ ET
BT 26.250 606.524 Td /F1 9.8 Tf  [(Bioinformatics. 2002 Jul;3\(1\):15. PubMed PMID: 11869452; PubMed Central PMCID: PMC65690.)] TJ ET
BT 26.250 587.119 Td /F1 9.8 Tf  [(29.)] TJ ET
BT 43.553 587.119 Td /F1 9.8 Tf  [(Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008 )] TJ ET
BT 26.250 575.214 Td /F1 9.8 Tf  [(Oct;57\(5\):758-71. PubMed PMID: 18853362.)] TJ ET
BT 26.250 555.810 Td /F1 9.8 Tf  [(30.)] TJ ET
BT 43.553 555.810 Td /F1 9.8 Tf  [(Katoh K, Toh H. PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. )] TJ ET
BT 26.250 543.905 Td /F1 9.8 Tf  [(Bioinformatics. 2007 Feb 1;23\(3\):372-4. Epub 2006 Nov 21. PubMed PMID: 17118958.)] TJ ET
BT 26.250 524.500 Td /F1 9.8 Tf  [(31.)] TJ ET
BT 43.553 524.500 Td /F1 9.8 Tf  [(Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids )] TJ ET
BT 26.250 512.595 Td /F1 9.8 Tf  [(Res. 1999 Jul 1;27\(13\):2682-90. PubMed PMID: 10373585; PubMed Central PMCID: PMC148477.)] TJ ET
BT 26.250 493.191 Td /F1 9.8 Tf  [(32.)] TJ ET
BT 43.553 493.191 Td /F1 9.8 Tf  [(Robinson DF, Foulds LR. Comparison of phylogenetic trees. Mathematical Biosciences. 1981; 53:131�147.)] TJ ET
BT 26.250 473.786 Td /F1 9.8 Tf  [(33.)] TJ ET
BT 43.553 473.786 Td /F1 9.8 Tf  [(Ott M, Zola J, Aluru S, Stamatakis A. Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. )] TJ ET
BT 26.250 461.881 Td /F1 9.8 Tf  [(Proceedings of ACM/IEEE Supercomputing Conference 2007. 2007.)] TJ ET
BT 26.250 442.476 Td /F1 9.8 Tf  [(34.)] TJ ET
BT 43.553 442.476 Td /F1 9.8 Tf  [(Litzkow M. Remote Unix - turning idle workstations into cycle servers. In Usenix Summer Conference, pages 381�384, )] TJ ET
BT 26.250 430.572 Td /F1 9.8 Tf  [(1987.)] TJ ET
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BT 26.250 767.476 Td /F1 9.8 Tf  [(Bioinformatics. 2006 Nov 1;22\(21\):2688-90. Epub 2006 Aug 23. PubMed PMID: 16928733.)] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(25.)] TJ ET
BT 43.553 748.071 Td /F1 9.8 Tf  [(Liu K, Linder CR, Warnow T. Supplementary online materials for PLoS Currents. Website, 2010. Available at )] TJ ET
BT 26.250 736.167 Td /F1 9.8 Tf  [(http://www.cs.utexas.edu/~phylo/datasets/tol/tol.html.)] TJ ET
BT 26.250 716.762 Td /F1 9.8 Tf  [(26.)] TJ ET
BT 43.553 716.762 Td /F1 9.8 Tf  [(Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance )] TJ ET
BT 26.250 704.857 Td /F1 9.8 Tf  [(matrix. Mol Biol Evol. 2009 Jul;26\(7\):1641-50. Epub 2009 Apr 17. PubMed PMID: 19377059; PubMed Central PMCID: )] TJ ET
BT 26.250 692.952 Td /F1 9.8 Tf  [(PMC2693737.)] TJ ET
BT 26.250 673.548 Td /F1 9.8 Tf  [(27.)] TJ ET
BT 43.553 673.548 Td /F1 9.8 Tf  [(Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010 )] TJ ET
BT 26.250 661.643 Td /F1 9.8 Tf  [(Mar 10;5\(3\):e9490. PubMed PMID: 20224823; PubMed Central PMCID: PMC2835736.)] TJ ET
BT 26.250 642.238 Td /F1 9.8 Tf  [(28.)] TJ ET
BT 43.553 642.238 Td /F1 9.8 Tf  [(Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, M�ller KM, Pande )] TJ ET
BT 26.250 630.333 Td /F1 9.8 Tf  [(N, Shang Z, Yu N, Gutell RR. The comparative RNA web \(CRW\) site: an online database of comparative sequence and )] TJ ET
BT 26.250 618.429 Td /F1 9.8 Tf  [(structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2. Epub 2002 Jan 17. Erratum in: BMC )] TJ ET
BT 26.250 606.524 Td /F1 9.8 Tf  [(Bioinformatics. 2002 Jul;3\(1\):15. PubMed PMID: 11869452; PubMed Central PMCID: PMC65690.)] TJ ET
BT 26.250 587.119 Td /F1 9.8 Tf  [(29.)] TJ ET
BT 43.553 587.119 Td /F1 9.8 Tf  [(Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008 )] TJ ET
BT 26.250 575.214 Td /F1 9.8 Tf  [(Oct;57\(5\):758-71. PubMed PMID: 18853362.)] TJ ET
BT 26.250 555.810 Td /F1 9.8 Tf  [(30.)] TJ ET
BT 43.553 555.810 Td /F1 9.8 Tf  [(Katoh K, Toh H. PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. )] TJ ET
BT 26.250 543.905 Td /F1 9.8 Tf  [(Bioinformatics. 2007 Feb 1;23\(3\):372-4. Epub 2006 Nov 21. PubMed PMID: 17118958.)] TJ ET
BT 26.250 524.500 Td /F1 9.8 Tf  [(31.)] TJ ET
BT 43.553 524.500 Td /F1 9.8 Tf  [(Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids )] TJ ET
BT 26.250 512.595 Td /F1 9.8 Tf  [(Res. 1999 Jul 1;27\(13\):2682-90. PubMed PMID: 10373585; PubMed Central PMCID: PMC148477.)] TJ ET
BT 26.250 493.191 Td /F1 9.8 Tf  [(32.)] TJ ET
BT 43.553 493.191 Td /F1 9.8 Tf  [(Robinson DF, Foulds LR. Comparison of phylogenetic trees. Mathematical Biosciences. 1981; 53:131�147.)] TJ ET
BT 26.250 473.786 Td /F1 9.8 Tf  [(33.)] TJ ET
BT 43.553 473.786 Td /F1 9.8 Tf  [(Ott M, Zola J, Aluru S, Stamatakis A. Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. )] TJ ET
BT 26.250 461.881 Td /F1 9.8 Tf  [(Proceedings of ACM/IEEE Supercomputing Conference 2007. 2007.)] TJ ET
BT 26.250 442.476 Td /F1 9.8 Tf  [(34.)] TJ ET
BT 43.553 442.476 Td /F1 9.8 Tf  [(Litzkow M. Remote Unix - turning idle workstations into cycle servers. In Usenix Summer Conference, pages 381�384, )] TJ ET
BT 26.250 430.572 Td /F1 9.8 Tf  [(1987.)] TJ ET
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BT 291.710 19.825 Td /F1 11.0 Tf  [(12)] TJ ET
BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

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