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BT 15.000 718.042 Td /F2 21.0 Tf  [(Benchmark datasets and software for developing and testing )] TJ ET
BT 15.000 693.094 Td /F2 21.0 Tf  [(methods for large-scale multiple sequence alignment and )] TJ ET
BT 15.000 668.146 Td /F2 21.0 Tf  [(phylogenetic inference)] TJ ET
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BT 26.250 573.482 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 553.528 Td /F1 9.8 Tf  [(We have assembled a collection of web pages that contain benchmark datasets and software tools to enable the evaluation of )] TJ ET
BT 26.250 541.623 Td /F1 9.8 Tf  [(the accuracy and scalability of computational methods for estimating evolutionary relationships. They provide a resource to the )] TJ ET
BT 26.250 529.719 Td /F1 9.8 Tf  [(scientific community for development of new alignment and tree inference methods on very difficult datasets. The datasets are )] TJ ET
BT 26.250 517.814 Td /F1 9.8 Tf  [(intended to help address three problems: multiple sequence alignment, phylogeny estimation given aligned sequences, and )] TJ ET
BT 26.250 505.909 Td /F1 9.8 Tf  [(supertree estimation. Datasets from our work include empirical datasets with carefully curated alignments suitable for testing )] TJ ET
BT 26.250 494.004 Td /F1 9.8 Tf  [(alignment and phylogenetic methods for large-scale systematics studies. Links to other empirical datasets, lacking curated )] TJ ET
BT 26.250 482.100 Td /F1 9.8 Tf  [(alignments, are also provided. We also include simulated datasets with properties typical of large-scale systematics studies, )] TJ ET
BT 26.250 470.195 Td /F1 9.8 Tf  [(including high rates of substitutions and indels, and we include the true alignment and tree for each simulated dataset. Finally, )] TJ ET
BT 26.250 458.290 Td /F1 9.8 Tf  [(we provide links to software tools for generating simulated datasets, and for evaluating the accuracy of alignments and trees )] TJ ET
BT 26.250 446.385 Td /F1 9.8 Tf  [(estimated on these datasets. We welcome contributions to the benchmark datasets from other researchers.)] TJ ET
BT 26.250 409.783 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 389.829 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 545.954 389.829 Td /F1 9.8 Tf  [(support )] TJ ET
BT 26.250 377.924 Td /F1 9.8 Tf  [(to TW.)] TJ ET
BT 26.250 366.019 Td /F1 9.8 Tf  [(One of the principal goals of the National Science Foundation�s Assembling the Tree of Life \(AToL\) initiative is �[a]ssembly of a )] TJ ET
BT 26.250 354.114 Td /F1 9.8 Tf  [(framework phylogeny, or Tree of Life, for all major lineages of life.� )] TJ ET
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BT 325.906 354.114 Td /F1 9.8 Tf  [( Much of that effort has focused on accumulating and )] TJ ET
BT 26.250 342.210 Td /F1 9.8 Tf  [(analyzing data for the major taxonomic groups. However, because of the scale of the problems \(numbers of species and )] TJ ET
BT 26.250 330.305 Td /F1 9.8 Tf  [(amount of sequence information\), the initiative has also required development of methods for sequence alignment, phylogenetic )] TJ ET
BT 26.250 318.400 Td /F1 9.8 Tf  [(inference and supertree estimation that can handle hundreds, thousands or even tens of thousands of sequences. In the last )] TJ ET
BT 26.250 306.495 Td /F1 9.8 Tf  [(decade, many new methods have been developed to address these challenging computational problems, including RAxML )] TJ ET
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BT 228.397 294.591 Td /F1 9.8 Tf  [(. However, evaluations of the efficacy of these methods for large-scale alignment )] TJ ET
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BT 26.250 263.281 Td /F1 9.8 Tf  [(To facilitate testing of large-scale alignment and phylogeny estimation methods, we have assembled a collection of web pages )] TJ ET
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BT 26.250 203.757 Td /F1 9.8 Tf  [(provide range in numbers of taxa from a few hundred to more than 300,000 sequences. The datasets are broken down into sets )] TJ ET
BT 26.250 191.853 Td /F1 9.8 Tf  [(most appropriate for three types of phylogenetic problems: phylogenetic estimation given aligned sequences, supertree )] TJ ET
BT 26.250 179.948 Td /F1 9.8 Tf  [(estimation, and multiple sequence alignment. Some datasets are appropriate for more than one type of problem and therefore )] TJ ET
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BT 26.250 131.441 Td /F4 12.0 Tf  [(Benchmarks for phylogenetic estimation)] TJ ET
BT 26.250 111.486 Td /F1 9.8 Tf  [(The benchmark datasets for phylogenetic estimation are both empirical and simulated. They have been used in large-scale )] TJ ET
BT 26.250 99.582 Td /F1 9.8 Tf  [(systematics studies, and so present challenges for maximum likelihood, maximum parsimony and Bayesian estimation. A )] TJ ET
BT 26.250 87.677 Td /F1 9.8 Tf  [(subset of the empirical datasets \(Table 1\) include curated alignments and reference trees \(generated using RAxML version )] TJ ET
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BT 61.486 75.772 Td /F1 9.8 Tf  [(\). Reference trees have been assessed by bootstrapping, with edges having less than 75% support contracted. The )] TJ ET
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BT 26.250 51.963 Td /F1 9.8 Tf  [(alignment and phylogenetic software to operate on large and/or difficult datasets. They can also be used to compare how well )] TJ ET
BT 26.250 40.058 Td /F1 9.8 Tf  [(algorithms solve particular optimality criteria, e.g., maximum parsimony or maximum likelihood. The empirical datasets include )] TJ ET
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BT 99.404 638.299 Td /F1 9.8 Tf  [(, )] TJ ET
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BT 104.825 638.299 Td /F1 9.8 Tf  [(Rahul Suri)] TJ ET
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BT 155.759 638.299 Td /F1 9.8 Tf  [(Kevin Liu)] TJ ET
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BT 26.250 626.394 Td /F1 9.8 Tf  [(Linder CR, Suri R, Liu K, Warnow T. Benchmark datasets and software for developing and testing methods for large-scale )] TJ ET
BT 26.250 614.490 Td /F1 9.8 Tf  [(multiple sequence alignment and phylogenetic inference. PLOS Currents Tree of Life. 2010 Nov 18 . Edition 1. doi: )] TJ ET
BT 26.250 602.585 Td /F1 9.8 Tf  [(10.1371/currents.RRN1195.)] TJ ET
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BT 26.250 573.482 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 553.528 Td /F1 9.8 Tf  [(We have assembled a collection of web pages that contain benchmark datasets and software tools to enable the evaluation of )] TJ ET
BT 26.250 541.623 Td /F1 9.8 Tf  [(the accuracy and scalability of computational methods for estimating evolutionary relationships. They provide a resource to the )] TJ ET
BT 26.250 529.719 Td /F1 9.8 Tf  [(scientific community for development of new alignment and tree inference methods on very difficult datasets. The datasets are )] TJ ET
BT 26.250 517.814 Td /F1 9.8 Tf  [(intended to help address three problems: multiple sequence alignment, phylogeny estimation given aligned sequences, and )] TJ ET
BT 26.250 505.909 Td /F1 9.8 Tf  [(supertree estimation. Datasets from our work include empirical datasets with carefully curated alignments suitable for testing )] TJ ET
BT 26.250 494.004 Td /F1 9.8 Tf  [(alignment and phylogenetic methods for large-scale systematics studies. Links to other empirical datasets, lacking curated )] TJ ET
BT 26.250 482.100 Td /F1 9.8 Tf  [(alignments, are also provided. We also include simulated datasets with properties typical of large-scale systematics studies, )] TJ ET
BT 26.250 470.195 Td /F1 9.8 Tf  [(including high rates of substitutions and indels, and we include the true alignment and tree for each simulated dataset. Finally, )] TJ ET
BT 26.250 458.290 Td /F1 9.8 Tf  [(we provide links to software tools for generating simulated datasets, and for evaluating the accuracy of alignments and trees )] TJ ET
BT 26.250 446.385 Td /F1 9.8 Tf  [(estimated on these datasets. We welcome contributions to the benchmark datasets from other researchers.)] TJ ET
BT 26.250 409.783 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 389.829 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 545.954 389.829 Td /F1 9.8 Tf  [(support )] TJ ET
BT 26.250 377.924 Td /F1 9.8 Tf  [(to TW.)] TJ ET
BT 26.250 366.019 Td /F1 9.8 Tf  [(One of the principal goals of the National Science Foundation�s Assembling the Tree of Life \(AToL\) initiative is �[a]ssembly of a )] TJ ET
BT 26.250 354.114 Td /F1 9.8 Tf  [(framework phylogeny, or Tree of Life, for all major lineages of life.� )] TJ ET
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BT 315.065 354.114 Td /F1 9.8 Tf  [([1])] TJ ET
0.271 0.267 0.267 rg
BT 325.906 354.114 Td /F1 9.8 Tf  [( Much of that effort has focused on accumulating and )] TJ ET
BT 26.250 342.210 Td /F1 9.8 Tf  [(analyzing data for the major taxonomic groups. However, because of the scale of the problems \(numbers of species and )] TJ ET
BT 26.250 330.305 Td /F1 9.8 Tf  [(amount of sequence information\), the initiative has also required development of methods for sequence alignment, phylogenetic )] TJ ET
BT 26.250 318.400 Td /F1 9.8 Tf  [(inference and supertree estimation that can handle hundreds, thousands or even tens of thousands of sequences. In the last )] TJ ET
BT 26.250 306.495 Td /F1 9.8 Tf  [(decade, many new methods have been developed to address these challenging computational problems, including RAxML )] TJ ET
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BT 558.424 306.495 Td /F1 9.8 Tf  [([2])] TJ ET
0.271 0.267 0.267 rg
BT 569.266 306.495 Td /F1 9.8 Tf  [(, )] TJ ET
BT 26.250 294.591 Td /F1 9.8 Tf  [(GARLI )] TJ ET
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BT 58.220 294.591 Td /F1 9.8 Tf  [([3])] TJ ET
0.271 0.267 0.267 rg
BT 69.062 294.591 Td /F1 9.8 Tf  [(, POY )] TJ ET
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BT 97.786 294.591 Td /F1 9.8 Tf  [([4])] TJ ET
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BT 108.628 294.591 Td /F1 9.8 Tf  [(, SAT� )] TJ ET
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BT 141.144 294.591 Td /F1 9.8 Tf  [([5])] TJ ET
0.271 0.267 0.267 rg
BT 151.986 294.591 Td /F1 9.8 Tf  [(, and MrBayes )] TJ ET
0.267 0.267 0.267 rg
BT 217.555 294.591 Td /F1 9.8 Tf  [([6])] TJ ET
0.271 0.267 0.267 rg
BT 228.397 294.591 Td /F1 9.8 Tf  [(. However, evaluations of the efficacy of these methods for large-scale alignment )] TJ ET
BT 26.250 282.686 Td /F1 9.8 Tf  [(and tree estimation�required for highly accurate estimations of the Tree of Life�have lagged behind method development.)] TJ ET
BT 26.250 263.281 Td /F1 9.8 Tf  [(To facilitate testing of large-scale alignment and phylogeny estimation methods, we have assembled a collection of web pages )] TJ ET
BT 26.250 251.376 Td /F1 9.8 Tf  [(of \(1\) benchmark datasets and \(2\) software appropriate for creating new simulated benchmark datasets \()] TJ ET
0.267 0.267 0.267 rg
BT 26.250 239.472 Td /F1 9.8 Tf  [(http://www .cs.utexas.edu/users/phylo/datasets/)] TJ ET
0.271 0.267 0.267 rg
BT 232.180 239.472 Td /F1 9.8 Tf  [(\). Because these datasets have been assembled with an eye to their usefulness )] TJ ET
BT 26.250 227.567 Td /F1 9.8 Tf  [(for Tree of Life-scale projects, only datasets that have large numbers of taxa and/or present other difficulties for phylogenetic )] TJ ET
BT 26.250 215.662 Td /F1 9.8 Tf  [(reconstruction and alignment \(e.g., high rates of substitution and insertions and deletions\) are included. The datasets we )] TJ ET
BT 26.250 203.757 Td /F1 9.8 Tf  [(provide range in numbers of taxa from a few hundred to more than 300,000 sequences. The datasets are broken down into sets )] TJ ET
BT 26.250 191.853 Td /F1 9.8 Tf  [(most appropriate for three types of phylogenetic problems: phylogenetic estimation given aligned sequences, supertree )] TJ ET
BT 26.250 179.948 Td /F1 9.8 Tf  [(estimation, and multiple sequence alignment. Some datasets are appropriate for more than one type of problem and therefore )] TJ ET
BT 26.250 168.043 Td /F1 9.8 Tf  [(are referenced more than once. Reference information and links are provided for all published datasets.)] TJ ET
BT 26.250 131.441 Td /F4 12.0 Tf  [(Benchmarks for phylogenetic estimation)] TJ ET
BT 26.250 111.486 Td /F1 9.8 Tf  [(The benchmark datasets for phylogenetic estimation are both empirical and simulated. They have been used in large-scale )] TJ ET
BT 26.250 99.582 Td /F1 9.8 Tf  [(systematics studies, and so present challenges for maximum likelihood, maximum parsimony and Bayesian estimation. A )] TJ ET
BT 26.250 87.677 Td /F1 9.8 Tf  [(subset of the empirical datasets \(Table 1\) include curated alignments and reference trees \(generated using RAxML version )] TJ ET
BT 26.250 75.772 Td /F1 9.8 Tf  [(7.0.4 )] TJ ET
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BT 50.645 75.772 Td /F1 9.8 Tf  [([2])] TJ ET
0.271 0.267 0.267 rg
BT 61.486 75.772 Td /F1 9.8 Tf  [(\). Reference trees have been assessed by bootstrapping, with edges having less than 75% support contracted. The )] TJ ET
BT 26.250 63.867 Td /F1 9.8 Tf  [(remaining empirical datasets lack curated alignments and reference trees, but are appropriate for assessing the ability of )] TJ ET
BT 26.250 51.963 Td /F1 9.8 Tf  [(alignment and phylogenetic software to operate on large and/or difficult datasets. They can also be used to compare how well )] TJ ET
BT 26.250 40.058 Td /F1 9.8 Tf  [(algorithms solve particular optimality criteria, e.g., maximum parsimony or maximum likelihood. The empirical datasets include )] TJ ET
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BT 15.000 693.094 Td /F2 21.0 Tf  [(methods for large-scale multiple sequence alignment and )] TJ ET
BT 15.000 668.146 Td /F2 21.0 Tf  [(phylogenetic inference)] TJ ET
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BT 96.510 650.140 Td /F3 9.8 Tf  [(�)] TJ ET
0.267 0.267 0.267 rg
BT 101.385 650.140 Td /F3 9.8 Tf  [(Tree of Life)] TJ ET
BT 26.250 638.299 Td /F1 9.8 Tf  [(C. Randal Linder)] TJ ET
0.271 0.267 0.267 rg
BT 99.404 638.299 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 104.825 638.299 Td /F1 9.8 Tf  [(Rahul Suri)] TJ ET
0.271 0.267 0.267 rg
BT 150.338 638.299 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 155.759 638.299 Td /F1 9.8 Tf  [(Kevin Liu)] TJ ET
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BT 195.861 638.299 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 201.282 638.299 Td /F1 9.8 Tf  [(Tandy Warnow)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 626.394 Td /F1 9.8 Tf  [(Linder CR, Suri R, Liu K, Warnow T. Benchmark datasets and software for developing and testing methods for large-scale )] TJ ET
BT 26.250 614.490 Td /F1 9.8 Tf  [(multiple sequence alignment and phylogenetic inference. PLOS Currents Tree of Life. 2010 Nov 18 . Edition 1. doi: )] TJ ET
BT 26.250 602.585 Td /F1 9.8 Tf  [(10.1371/currents.RRN1195.)] TJ ET
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BT 26.250 573.482 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 553.528 Td /F1 9.8 Tf  [(We have assembled a collection of web pages that contain benchmark datasets and software tools to enable the evaluation of )] TJ ET
BT 26.250 541.623 Td /F1 9.8 Tf  [(the accuracy and scalability of computational methods for estimating evolutionary relationships. They provide a resource to the )] TJ ET
BT 26.250 529.719 Td /F1 9.8 Tf  [(scientific community for development of new alignment and tree inference methods on very difficult datasets. The datasets are )] TJ ET
BT 26.250 517.814 Td /F1 9.8 Tf  [(intended to help address three problems: multiple sequence alignment, phylogeny estimation given aligned sequences, and )] TJ ET
BT 26.250 505.909 Td /F1 9.8 Tf  [(supertree estimation. Datasets from our work include empirical datasets with carefully curated alignments suitable for testing )] TJ ET
BT 26.250 494.004 Td /F1 9.8 Tf  [(alignment and phylogenetic methods for large-scale systematics studies. Links to other empirical datasets, lacking curated )] TJ ET
BT 26.250 482.100 Td /F1 9.8 Tf  [(alignments, are also provided. We also include simulated datasets with properties typical of large-scale systematics studies, )] TJ ET
BT 26.250 470.195 Td /F1 9.8 Tf  [(including high rates of substitutions and indels, and we include the true alignment and tree for each simulated dataset. Finally, )] TJ ET
BT 26.250 458.290 Td /F1 9.8 Tf  [(we provide links to software tools for generating simulated datasets, and for evaluating the accuracy of alignments and trees )] TJ ET
BT 26.250 446.385 Td /F1 9.8 Tf  [(estimated on these datasets. We welcome contributions to the benchmark datasets from other researchers.)] TJ ET
BT 26.250 409.783 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 389.829 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 545.954 389.829 Td /F1 9.8 Tf  [(support )] TJ ET
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BT 644.625 515.207 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
32.625 503.331 94.500 0.750 re f
32.625 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 39.375 485.115 Td /F1 9.8 Tf  [(23S.E.aa_ag )] TJ ET
BT 98.460 487.680 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
126.375 503.331 85.500 0.750 re f
126.375 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 133.125 487.476 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 503.331 175.500 0.750 re f
211.125 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 217.875 487.476 Td /F1 9.8 Tf  [(Eukaryotes nuclear)] TJ ET
0.267 0.267 0.267 rg
385.875 503.331 84.750 0.750 re f
385.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 392.625 487.476 Td /F1 9.8 Tf  [(144)] TJ ET
0.267 0.267 0.267 rg
469.875 503.331 84.750 0.750 re f
469.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 476.625 487.476 Td /F1 9.8 Tf  [(8,619)] TJ ET
0.267 0.267 0.267 rg
553.875 503.331 84.750 0.750 re f
553.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 560.625 487.476 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
637.875 503.331 85.500 0.750 re f
637.875 475.599 0.750 28.482 re f
722.625 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 644.625 487.476 Td /F1 9.8 Tf  [(13.5)] TJ ET
0.267 0.267 0.267 rg
32.625 475.599 94.125 0.750 re f
32.625 450.942 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 39.000 460.119 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
126.750 475.599 84.750 0.750 re f
0.271 0.267 0.267 rg
BT 132.750 460.119 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.500 475.599 174.750 0.750 re f
0.271 0.267 0.267 rg
BT 217.500 460.119 Td /F1 9.8 Tf  [(Eukaryotes)] TJ ET
0.267 0.267 0.267 rg
386.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 392.250 460.119 Td /F1 9.8 Tf  [(117)] TJ ET
0.267 0.267 0.267 rg
470.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 476.250 460.119 Td /F1 9.8 Tf  [(9,079)] TJ ET
0.267 0.267 0.267 rg
554.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 560.250 460.119 Td /F1 9.8 Tf  [(59.7)] TJ ET
0.267 0.267 0.267 rg
638.250 475.599 85.125 0.750 re f
722.625 450.942 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 644.250 460.119 Td /F1 9.8 Tf  [(12.6)] TJ ET
0.000 0.000 0.000 rg
32.625 450.942 94.125 1.000 re f
0.267 0.267 0.267 rg
32.625 386.784 94.125 0.750 re f
0.000 0.000 0.000 rg
126.750 450.942 84.750 1.000 re f
0.267 0.267 0.267 rg
126.750 386.784 84.750 0.750 re f
0.000 0.000 0.000 rg
211.500 450.942 174.750 1.000 re f
0.267 0.267 0.267 rg
211.500 386.784 174.750 0.750 re f
0.000 0.000 0.000 rg
386.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
386.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
470.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
470.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
554.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
554.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
638.250 450.942 85.125 1.000 re f
0.267 0.267 0.267 rg
638.250 386.784 85.125 0.750 re f
32.625 386.784 0.750 65.159 re f
722.625 386.784 0.750 65.159 re f
0.271 0.267 0.267 rg
BT 39.375 435.292 Td /F1 8.7 Tf  [(a)] TJ ET
BT 44.194 432.727 Td /F1 9.8 Tf  [( Unless otherwise noted, all datasets in this table are taken from Cannone et al. )] TJ ET
0.267 0.267 0.267 rg
BT 389.402 432.727 Td /F1 9.8 Tf  [([7])] TJ ET
0.271 0.267 0.267 rg
BT 400.244 432.727 Td /F1 9.8 Tf  [(. Curated alignments were produced by Cannone et al. using covariation )] TJ ET
BT 39.375 424.505 Td /F1 9.8 Tf  [(and secondary structure. The reference trees reported on our web site were generated using RAxML version 7.0.4. Complete run parameters and program )] TJ ET
BT 39.375 416.874 Td /F1 9.8 Tf  [(commands are listed on the web site.)] TJ ET
BT 39.375 409.447 Td /F1 8.7 Tf  [(b)] TJ ET
BT 44.194 406.882 Td /F1 9.8 Tf  [( The number of columns in the aligned dataset. )] TJ ET
BT 39.375 398.865 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
BT 43.708 396.300 Td /F1 9.8 Tf  [([8])] TJ ET
0.271 0.267 0.267 rg
BT 26.250 339.385 Td /F1 9.8 Tf  [(Simulated datasets \(Table 2\) were taken from three sources and include both amino acid and nucleil acid sequences of widely )] TJ ET
BT 26.250 327.480 Td /F1 9.8 Tf  [(varying numbers of sequences, rates of substitution and sizes and rates of indels.)] TJ ET
1.000 1.000 1.000 rg
32.250 120.903 833.250 196.696 re f
0.267 0.267 0.267 rg
32.625 316.474 110.375 0.750 re f
143.000 316.474 197.250 0.750 re f
340.250 316.474 110.000 0.750 re f
450.250 316.474 111.750 0.750 re f
562.000 316.474 110.000 0.750 re f
672.000 316.474 193.125 0.750 re f
32.625 291.818 0.750 25.406 re f
864.375 291.818 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 39.000 300.994 Td /F4 9.8 Tf  [(Table 2)] TJ ET
BT 72.599 300.994 Td /F1 9.8 Tf  [( . Simulated sequence datasets and some of their properties.)] TJ ET
0.000 0.000 0.000 rg
32.625 291.818 110.375 1.000 re f
0.267 0.267 0.267 rg
32.625 256.705 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 39.000 276.463 Td /F4 9.8 Tf  [(Dataset)] TJ ET
0.000 0.000 0.000 rg
143.000 291.818 197.250 1.000 re f
0.271 0.267 0.267 rg
BT 149.000 276.463 Td /F4 9.8 Tf  [(Source)] TJ ET
0.000 0.000 0.000 rg
340.250 291.818 110.000 1.000 re f
0.271 0.267 0.267 rg
BT 346.250 274.102 Td /F4 9.8 Tf  [(Data Type)] TJ ET
BT 392.845 276.668 Td /F4 8.7 Tf  [(a)] TJ ET
0.000 0.000 0.000 rg
450.250 291.818 111.750 1.000 re f
0.271 0.267 0.267 rg
BT 456.250 276.463 Td /F4 9.8 Tf  [(Number of Taxa)] TJ ET
0.000 0.000 0.000 rg
562.000 291.818 110.000 1.000 re f
0.271 0.267 0.267 rg
BT 568.000 276.463 Td /F4 9.8 Tf  [(Number of )] TJ ET
BT 568.000 266.471 Td /F4 9.8 Tf  [(Characters)] TJ ET
BT 618.934 269.036 Td /F4 8.7 Tf  [(b)] TJ ET
0.000 0.000 0.000 rg
672.000 291.818 193.125 1.000 re f
0.267 0.267 0.267 rg
864.375 256.705 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 678.000 274.102 Td /F4 9.8 Tf  [(Software)] TJ ET
BT 719.174 276.668 Td /F4 8.7 Tf  [(c)] TJ ET
0.000 0.000 0.000 rg
32.625 256.705 110.750 1.000 re f
0.267 0.267 0.267 rg
32.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 39.375 240.850 Td /F1 9.8 Tf  [(FastTree)] TJ ET
0.000 0.000 0.000 rg
142.625 256.705 198.000 1.000 re f
0.267 0.267 0.267 rg
142.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 149.375 240.850 Td /F1 9.8 Tf  [(Price et al. )] TJ ET
0.267 0.267 0.267 rg
BT 198.144 240.850 Td /F1 9.8 Tf  [([9])] TJ ET
0.271 0.267 0.267 rg
BT 149.375 233.219 Td /F1 9.8 Tf  [(Price et al. )] TJ ET
0.267 0.267 0.267 rg
BT 198.144 233.219 Td /F1 9.8 Tf  [([10])] TJ ET
0.000 0.000 0.000 rg
339.875 256.705 110.750 1.000 re f
0.267 0.267 0.267 rg
339.875 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 346.625 240.850 Td /F1 9.8 Tf  [(AA )] TJ ET
BT 346.625 233.219 Td /F1 9.8 Tf  [(NA)] TJ ET
0.000 0.000 0.000 rg
449.875 256.705 112.500 1.000 re f
0.267 0.267 0.267 rg
449.875 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 456.625 240.850 Td /F1 9.8 Tf  [(250; 1,250; )] TJ ET
BT 456.625 233.219 Td /F1 9.8 Tf  [(5,00078,132)] TJ ET
0.000 0.000 0.000 rg
561.625 256.705 110.750 1.000 re f
0.267 0.267 0.267 rg
561.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 568.375 240.850 Td /F1 9.8 Tf  [(N/A)] TJ ET
0.000 0.000 0.000 rg
671.625 256.705 193.500 1.000 re f
0.267 0.267 0.267 rg
671.625 224.292 0.750 33.413 re f
864.375 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 678.375 240.850 Td /F1 9.8 Tf  [(Rose )] TJ ET
0.267 0.267 0.267 rg
BT 703.842 240.850 Td /F1 9.8 Tf  [([11])] TJ ET
32.625 224.292 110.750 0.750 re f
32.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 39.375 208.437 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
142.625 224.292 198.000 0.750 re f
142.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 149.375 208.437 Td /F1 9.8 Tf  [(Liu et al. )] TJ ET
0.267 0.267 0.267 rg
BT 188.940 208.437 Td /F1 9.8 Tf  [([5])] TJ ET
339.875 224.292 110.750 0.750 re f
339.875 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 346.625 208.437 Td /F1 9.8 Tf  [(NA)] TJ ET
0.267 0.267 0.267 rg
449.875 224.292 112.500 0.750 re f
449.875 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 456.625 208.437 Td /F1 9.8 Tf  [(100; 500; 1,000)] TJ ET
0.267 0.267 0.267 rg
561.625 224.292 110.750 0.750 re f
561.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 568.375 208.437 Td /F1 9.8 Tf  [(1,000)] TJ ET
0.267 0.267 0.267 rg
671.625 224.292 193.500 0.750 re f
671.625 199.511 0.750 25.531 re f
864.375 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 678.375 208.437 Td /F1 9.8 Tf  [(SeqGen )] TJ ET
0.267 0.267 0.267 rg
BT 716.858 208.437 Td /F1 9.8 Tf  [([12])] TJ ET
0.271 0.267 0.267 rg
BT 733.121 208.437 Td /F1 9.8 Tf  [( Rose )] TJ ET
0.267 0.267 0.267 rg
BT 761.299 208.437 Td /F1 9.8 Tf  [([11])] TJ ET
32.625 199.511 110.375 0.750 re f
32.625 159.592 0.750 40.669 re f
0.271 0.267 0.267 rg
BT 39.000 184.031 Td /F1 9.8 Tf  [(RNASim)] TJ ET
0.267 0.267 0.267 rg
143.000 199.511 197.250 0.750 re f
BT 149.000 184.031 Td /F1 9.8 Tf  [(kim.bio.upenn.edu/software/csd.shtml)] TJ ET
340.250 199.511 110.000 0.750 re f
0.271 0.267 0.267 rg
BT 346.250 184.031 Td /F1 9.8 Tf  [(NA \(SSU rRNA\))] TJ ET
0.267 0.267 0.267 rg
450.250 199.511 111.750 0.750 re f
0.271 0.267 0.267 rg
BT 456.250 184.031 Td /F1 9.8 Tf  [(128; 256; 512; 1,024; )] TJ ET
BT 456.250 176.400 Td /F1 9.8 Tf  [(2,048; 4,096; 8,192; )] TJ ET
BT 456.250 168.769 Td /F1 9.8 Tf  [(16,384; 1,000,000)] TJ ET
0.267 0.267 0.267 rg
562.000 199.511 110.000 0.750 re f
0.271 0.267 0.267 rg
BT 568.000 184.031 Td /F1 9.8 Tf  [(1,542)] TJ ET
0.267 0.267 0.267 rg
672.000 199.511 193.125 0.750 re f
864.375 159.592 0.750 40.669 re f
0.271 0.267 0.267 rg
BT 678.000 184.031 Td /F1 9.8 Tf  [(RNASim )] TJ ET
0.267 0.267 0.267 rg
BT 718.082 184.031 Td /F1 9.8 Tf  [([13])] TJ ET
0.000 0.000 0.000 rg
32.625 159.592 110.375 1.000 re f
0.267 0.267 0.267 rg
32.625 121.278 110.375 0.750 re f
0.000 0.000 0.000 rg
143.000 159.592 197.250 1.000 re f
0.267 0.267 0.267 rg
143.000 121.278 197.250 0.750 re f
0.000 0.000 0.000 rg
340.250 159.592 110.000 1.000 re f
0.267 0.267 0.267 rg
340.250 121.278 110.000 0.750 re f
0.000 0.000 0.000 rg
450.250 159.592 111.750 1.000 re f
0.267 0.267 0.267 rg
450.250 121.278 111.750 0.750 re f
0.000 0.000 0.000 rg
562.000 159.592 110.000 1.000 re f
0.267 0.267 0.267 rg
562.000 121.278 110.000 0.750 re f
0.000 0.000 0.000 rg
672.000 159.592 193.125 1.000 re f
0.267 0.267 0.267 rg
672.000 121.278 193.125 0.750 re f
32.625 121.278 0.750 39.314 re f
864.375 121.278 0.750 39.314 re f
0.271 0.267 0.267 rg
BT 39.375 143.942 Td /F1 8.7 Tf  [(a)] TJ ET
BT 44.194 141.377 Td /F1 9.8 Tf  [( AA = amino acid; NA = nucleic acid)] TJ ET
BT 199.180 143.942 Td /F1 8.7 Tf  [(b)] TJ ET
BT 203.998 141.377 Td /F1 9.8 Tf  [( The number of characters in the root sequence)] TJ ET
BT 39.375 133.360 Td /F1 8.7 Tf  [(c)] TJ ET
BT 43.708 130.795 Td /F1 9.8 Tf  [( The software used to generate the datasets)] TJ ET
BT 26.250 56.682 Td /F4 12.0 Tf  [(Benchmarks for multiple sequence alignment)] TJ ET
BT 26.250 36.727 Td /F1 9.8 Tf  [(Most of the benchmark datasets for multiple sequence alignment are the same as those for phylogenetic estimation. Both )] TJ ET
Q
q
15.000 22.442 577.500 754.558 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(both nucleic acid and amino acid sequence data.)] TJ ET
1.000 1.000 1.000 rg
32.250 386.409 691.500 371.187 re f
0.267 0.267 0.267 rg
32.625 756.470 94.125 0.750 re f
126.750 756.470 84.750 0.750 re f
211.500 756.470 174.750 0.750 re f
386.250 756.470 84.000 0.750 re f
470.250 756.470 84.000 0.750 re f
554.250 756.470 84.000 0.750 re f
638.250 756.470 85.125 0.750 re f
32.625 731.814 0.750 25.406 re f
722.625 731.814 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 39.000 740.990 Td /F4 9.8 Tf  [(Table 1)] TJ ET
BT 72.599 740.990 Td /F1 9.8 Tf  [( . Empirical datasets and their properties.)] TJ ET
0.000 0.000 0.000 rg
32.625 731.814 94.125 1.000 re f
0.267 0.267 0.267 rg
32.625 696.701 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 39.000 714.098 Td /F4 9.8 Tf  [(Dataset)] TJ ET
BT 74.217 716.664 Td /F4 8.7 Tf  [(a)] TJ ET
0.000 0.000 0.000 rg
126.750 731.814 84.750 1.000 re f
0.271 0.267 0.267 rg
BT 132.750 716.459 Td /F4 9.8 Tf  [(Gene)] TJ ET
0.000 0.000 0.000 rg
211.500 731.814 174.750 1.000 re f
0.271 0.267 0.267 rg
BT 217.500 716.459 Td /F4 9.8 Tf  [(Taxonomic Range)] TJ ET
0.000 0.000 0.000 rg
386.250 731.814 84.000 1.000 re f
0.271 0.267 0.267 rg
BT 392.250 716.459 Td /F4 9.8 Tf  [(Number of )] TJ ET
BT 392.250 708.828 Td /F4 9.8 Tf  [(Taxa)] TJ ET
0.000 0.000 0.000 rg
470.250 731.814 84.000 1.000 re f
0.271 0.267 0.267 rg
BT 476.250 716.459 Td /F4 9.8 Tf  [(Number of )] TJ ET
BT 476.250 706.467 Td /F4 9.8 Tf  [(Characters)] TJ ET
BT 527.184 709.032 Td /F4 8.7 Tf  [(b)] TJ ET
0.000 0.000 0.000 rg
554.250 731.814 84.000 1.000 re f
0.271 0.267 0.267 rg
BT 560.250 716.459 Td /F4 9.8 Tf  [(Percentage )] TJ ET
BT 560.250 708.828 Td /F4 9.8 Tf  [(Indels)] TJ ET
0.000 0.000 0.000 rg
638.250 731.814 85.125 1.000 re f
0.267 0.267 0.267 rg
722.625 696.701 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 644.250 716.459 Td /F4 9.8 Tf  [(Average Gap )] TJ ET
BT 644.250 708.828 Td /F4 9.8 Tf  [(Length)] TJ ET
0.000 0.000 0.000 rg
32.625 696.701 94.500 1.000 re f
0.267 0.267 0.267 rg
32.625 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 39.375 680.846 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.000 0.000 0.000 rg
126.375 696.701 85.500 1.000 re f
0.267 0.267 0.267 rg
126.375 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 133.125 680.846 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.000 0.000 0.000 rg
211.125 696.701 175.500 1.000 re f
0.267 0.267 0.267 rg
211.125 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 217.875 680.846 Td /F1 9.8 Tf  [(Bacteria)] TJ ET
0.000 0.000 0.000 rg
385.875 696.701 84.750 1.000 re f
0.267 0.267 0.267 rg
385.875 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 392.625 680.846 Td /F1 9.8 Tf  [(27,643)] TJ ET
0.000 0.000 0.000 rg
469.875 696.701 84.750 1.000 re f
0.267 0.267 0.267 rg
469.875 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 476.625 680.846 Td /F1 9.8 Tf  [(6,857)] TJ ET
0.000 0.000 0.000 rg
553.875 696.701 84.750 1.000 re f
0.267 0.267 0.267 rg
553.875 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 560.625 680.846 Td /F1 9.8 Tf  [(80.0)] TJ ET
0.000 0.000 0.000 rg
637.875 696.701 85.500 1.000 re f
0.267 0.267 0.267 rg
637.875 671.919 0.750 25.781 re f
722.625 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 644.625 680.846 Td /F1 9.8 Tf  [(4.9)] TJ ET
0.267 0.267 0.267 rg
32.625 671.919 94.500 0.750 re f
32.625 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 39.375 656.065 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
126.375 671.919 85.500 0.750 re f
126.375 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 133.125 656.065 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 671.919 175.500 0.750 re f
211.125 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 217.875 656.065 Td /F1 9.8 Tf  [(The three domains of life plus )] TJ ET
BT 217.875 648.433 Td /F1 9.8 Tf  [(mitochondria and chloroplasts)] TJ ET
0.267 0.267 0.267 rg
385.875 671.919 84.750 0.750 re f
385.875 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 392.625 656.065 Td /F1 9.8 Tf  [(7,350)] TJ ET
0.267 0.267 0.267 rg
469.875 671.919 84.750 0.750 re f
469.875 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 476.625 656.065 Td /F1 9.8 Tf  [(11,856)] TJ ET
0.267 0.267 0.267 rg
553.875 671.919 84.750 0.750 re f
553.875 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 560.625 656.065 Td /F1 9.8 Tf  [(87.4)] TJ ET
0.267 0.267 0.267 rg
637.875 671.919 85.500 0.750 re f
637.875 639.507 0.750 33.162 re f
722.625 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 644.625 656.065 Td /F1 9.8 Tf  [(12.1)] TJ ET
0.267 0.267 0.267 rg
32.625 639.507 94.500 0.750 re f
32.625 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 39.375 623.652 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
126.375 639.507 85.500 0.750 re f
126.375 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 133.125 623.652 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 639.507 175.500 0.750 re f
211.125 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 217.875 623.652 Td /F1 9.8 Tf  [(The three domains of life)] TJ ET
0.267 0.267 0.267 rg
385.875 639.507 84.750 0.750 re f
385.875 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 392.625 623.652 Td /F1 9.8 Tf  [(6,323)] TJ ET
0.267 0.267 0.267 rg
469.875 639.507 84.750 0.750 re f
469.875 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 476.625 623.652 Td /F1 9.8 Tf  [(8,716)] TJ ET
0.267 0.267 0.267 rg
553.875 639.507 84.750 0.750 re f
553.875 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 560.625 623.652 Td /F1 9.8 Tf  [(82.1)] TJ ET
0.267 0.267 0.267 rg
637.875 639.507 85.500 0.750 re f
637.875 614.726 0.750 25.531 re f
722.625 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 644.625 623.652 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
32.625 614.726 94.500 0.750 re f
32.625 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 39.375 596.510 Td /F1 9.8 Tf  [(16S.M.aa_ag )] TJ ET
BT 100.078 599.075 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
126.375 614.726 85.500 0.750 re f
126.375 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 133.125 598.871 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 614.726 175.500 0.750 re f
211.125 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 217.875 598.871 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 614.726 84.750 0.750 re f
385.875 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 392.625 598.871 Td /F1 9.8 Tf  [(1,028)] TJ ET
0.267 0.267 0.267 rg
469.875 614.726 84.750 0.750 re f
469.875 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 476.625 598.871 Td /F1 9.8 Tf  [(4,907)] TJ ET
0.267 0.267 0.267 rg
553.875 614.726 84.750 0.750 re f
553.875 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 560.625 598.871 Td /F1 9.8 Tf  [(82.6)] TJ ET
0.267 0.267 0.267 rg
637.875 614.726 85.500 0.750 re f
637.875 586.994 0.750 28.482 re f
722.625 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 644.625 598.871 Td /F1 9.8 Tf  [(22.0)] TJ ET
0.267 0.267 0.267 rg
32.625 586.994 94.500 0.750 re f
32.625 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 39.375 571.139 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
126.375 586.994 85.500 0.750 re f
126.375 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 133.125 571.139 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 586.994 175.500 0.750 re f
211.125 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 217.875 571.139 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 586.994 84.750 0.750 re f
385.875 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 392.625 571.139 Td /F1 9.8 Tf  [(901)] TJ ET
0.267 0.267 0.267 rg
469.875 586.994 84.750 0.750 re f
469.875 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 476.625 571.139 Td /F1 9.8 Tf  [(4,722)] TJ ET
0.267 0.267 0.267 rg
553.875 586.994 84.750 0.750 re f
553.875 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 560.625 571.139 Td /F1 9.8 Tf  [(78.1)] TJ ET
0.267 0.267 0.267 rg
637.875 586.994 85.500 0.750 re f
637.875 555.844 0.750 31.900 re f
722.625 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 644.625 571.139 Td /F1 9.8 Tf  [(17.2)] TJ ET
0.267 0.267 0.267 rg
32.625 555.844 94.500 0.750 re f
32.625 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 39.375 539.989 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
126.375 555.844 85.500 0.750 re f
126.375 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 133.125 539.989 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 555.844 175.500 0.750 re f
211.125 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 217.875 539.989 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 555.844 84.750 0.750 re f
385.875 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 392.625 539.989 Td /F1 9.8 Tf  [(278)] TJ ET
0.267 0.267 0.267 rg
469.875 555.844 84.750 0.750 re f
469.875 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 476.625 539.989 Td /F1 9.8 Tf  [(10,738)] TJ ET
0.267 0.267 0.267 rg
553.875 555.844 84.750 0.750 re f
553.875 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 560.625 539.989 Td /F1 9.8 Tf  [(83.7)] TJ ET
0.267 0.267 0.267 rg
637.875 555.844 85.500 0.750 re f
637.875 531.062 0.750 25.531 re f
722.625 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 644.625 539.989 Td /F1 9.8 Tf  [(31.9)] TJ ET
0.267 0.267 0.267 rg
32.625 531.062 94.500 0.750 re f
32.625 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 39.375 512.847 Td /F1 9.8 Tf  [(23S.M.aa_ag )] TJ ET
BT 100.078 515.412 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
126.375 531.062 85.500 0.750 re f
126.375 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 133.125 515.207 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 531.062 175.500 0.750 re f
211.125 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 217.875 515.207 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 531.062 84.750 0.750 re f
385.875 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 392.625 515.207 Td /F1 9.8 Tf  [(263)] TJ ET
0.267 0.267 0.267 rg
469.875 531.062 84.750 0.750 re f
469.875 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 476.625 515.207 Td /F1 9.8 Tf  [(10,305)] TJ ET
0.267 0.267 0.267 rg
553.875 531.062 84.750 0.750 re f
553.875 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 560.625 515.207 Td /F1 9.8 Tf  [(83.5)] TJ ET
0.267 0.267 0.267 rg
637.875 531.062 85.500 0.750 re f
637.875 503.331 0.750 28.482 re f
722.625 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 644.625 515.207 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
32.625 503.331 94.500 0.750 re f
32.625 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 39.375 485.115 Td /F1 9.8 Tf  [(23S.E.aa_ag )] TJ ET
BT 98.460 487.680 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
126.375 503.331 85.500 0.750 re f
126.375 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 133.125 487.476 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 503.331 175.500 0.750 re f
211.125 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 217.875 487.476 Td /F1 9.8 Tf  [(Eukaryotes nuclear)] TJ ET
0.267 0.267 0.267 rg
385.875 503.331 84.750 0.750 re f
385.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 392.625 487.476 Td /F1 9.8 Tf  [(144)] TJ ET
0.267 0.267 0.267 rg
469.875 503.331 84.750 0.750 re f
469.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 476.625 487.476 Td /F1 9.8 Tf  [(8,619)] TJ ET
0.267 0.267 0.267 rg
553.875 503.331 84.750 0.750 re f
553.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 560.625 487.476 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
637.875 503.331 85.500 0.750 re f
637.875 475.599 0.750 28.482 re f
722.625 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 644.625 487.476 Td /F1 9.8 Tf  [(13.5)] TJ ET
0.267 0.267 0.267 rg
32.625 475.599 94.125 0.750 re f
32.625 450.942 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 39.000 460.119 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
126.750 475.599 84.750 0.750 re f
0.271 0.267 0.267 rg
BT 132.750 460.119 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.500 475.599 174.750 0.750 re f
0.271 0.267 0.267 rg
BT 217.500 460.119 Td /F1 9.8 Tf  [(Eukaryotes)] TJ ET
0.267 0.267 0.267 rg
386.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 392.250 460.119 Td /F1 9.8 Tf  [(117)] TJ ET
0.267 0.267 0.267 rg
470.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 476.250 460.119 Td /F1 9.8 Tf  [(9,079)] TJ ET
0.267 0.267 0.267 rg
554.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 560.250 460.119 Td /F1 9.8 Tf  [(59.7)] TJ ET
0.267 0.267 0.267 rg
638.250 475.599 85.125 0.750 re f
722.625 450.942 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 644.250 460.119 Td /F1 9.8 Tf  [(12.6)] TJ ET
0.000 0.000 0.000 rg
32.625 450.942 94.125 1.000 re f
0.267 0.267 0.267 rg
32.625 386.784 94.125 0.750 re f
0.000 0.000 0.000 rg
126.750 450.942 84.750 1.000 re f
0.267 0.267 0.267 rg
126.750 386.784 84.750 0.750 re f
0.000 0.000 0.000 rg
211.500 450.942 174.750 1.000 re f
0.267 0.267 0.267 rg
211.500 386.784 174.750 0.750 re f
0.000 0.000 0.000 rg
386.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
386.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
470.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
470.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
554.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
554.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
638.250 450.942 85.125 1.000 re f
0.267 0.267 0.267 rg
638.250 386.784 85.125 0.750 re f
32.625 386.784 0.750 65.159 re f
722.625 386.784 0.750 65.159 re f
0.271 0.267 0.267 rg
BT 39.375 435.292 Td /F1 8.7 Tf  [(a)] TJ ET
BT 44.194 432.727 Td /F1 9.8 Tf  [( Unless otherwise noted, all datasets in this table are taken from Cannone et al. )] TJ ET
0.267 0.267 0.267 rg
BT 389.402 432.727 Td /F1 9.8 Tf  [([7])] TJ ET
0.271 0.267 0.267 rg
BT 400.244 432.727 Td /F1 9.8 Tf  [(. Curated alignments were produced by Cannone et al. using covariation )] TJ ET
BT 39.375 424.505 Td /F1 9.8 Tf  [(and secondary structure. The reference trees reported on our web site were generated using RAxML version 7.0.4. Complete run parameters and program )] TJ ET
BT 39.375 416.874 Td /F1 9.8 Tf  [(commands are listed on the web site.)] TJ ET
BT 39.375 409.447 Td /F1 8.7 Tf  [(b)] TJ ET
BT 44.194 406.882 Td /F1 9.8 Tf  [( The number of columns in the aligned dataset. )] TJ ET
BT 39.375 398.865 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
BT 43.708 396.300 Td /F1 9.8 Tf  [([8])] TJ ET
0.271 0.267 0.267 rg
BT 26.250 339.385 Td /F1 9.8 Tf  [(Simulated datasets \(Table 2\) were taken from three sources and include both amino acid and nucleil acid sequences of widely )] TJ ET
BT 26.250 327.480 Td /F1 9.8 Tf  [(varying numbers of sequences, rates of substitution and sizes and rates of indels.)] TJ ET
1.000 1.000 1.000 rg
32.250 120.903 833.250 196.696 re f
0.267 0.267 0.267 rg
32.625 316.474 110.375 0.750 re f
143.000 316.474 197.250 0.750 re f
340.250 316.474 110.000 0.750 re f
450.250 316.474 111.750 0.750 re f
562.000 316.474 110.000 0.750 re f
672.000 316.474 193.125 0.750 re f
32.625 291.818 0.750 25.406 re f
864.375 291.818 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 39.000 300.994 Td /F4 9.8 Tf  [(Table 2)] TJ ET
BT 72.599 300.994 Td /F1 9.8 Tf  [( . Simulated sequence datasets and some of their properties.)] TJ ET
0.000 0.000 0.000 rg
32.625 291.818 110.375 1.000 re f
0.267 0.267 0.267 rg
32.625 256.705 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 39.000 276.463 Td /F4 9.8 Tf  [(Dataset)] TJ ET
0.000 0.000 0.000 rg
143.000 291.818 197.250 1.000 re f
0.271 0.267 0.267 rg
BT 149.000 276.463 Td /F4 9.8 Tf  [(Source)] TJ ET
0.000 0.000 0.000 rg
340.250 291.818 110.000 1.000 re f
0.271 0.267 0.267 rg
BT 346.250 274.102 Td /F4 9.8 Tf  [(Data Type)] TJ ET
BT 392.845 276.668 Td /F4 8.7 Tf  [(a)] TJ ET
0.000 0.000 0.000 rg
450.250 291.818 111.750 1.000 re f
0.271 0.267 0.267 rg
BT 456.250 276.463 Td /F4 9.8 Tf  [(Number of Taxa)] TJ ET
0.000 0.000 0.000 rg
562.000 291.818 110.000 1.000 re f
0.271 0.267 0.267 rg
BT 568.000 276.463 Td /F4 9.8 Tf  [(Number of )] TJ ET
BT 568.000 266.471 Td /F4 9.8 Tf  [(Characters)] TJ ET
BT 618.934 269.036 Td /F4 8.7 Tf  [(b)] TJ ET
0.000 0.000 0.000 rg
672.000 291.818 193.125 1.000 re f
0.267 0.267 0.267 rg
864.375 256.705 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 678.000 274.102 Td /F4 9.8 Tf  [(Software)] TJ ET
BT 719.174 276.668 Td /F4 8.7 Tf  [(c)] TJ ET
0.000 0.000 0.000 rg
32.625 256.705 110.750 1.000 re f
0.267 0.267 0.267 rg
32.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 39.375 240.850 Td /F1 9.8 Tf  [(FastTree)] TJ ET
0.000 0.000 0.000 rg
142.625 256.705 198.000 1.000 re f
0.267 0.267 0.267 rg
142.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 149.375 240.850 Td /F1 9.8 Tf  [(Price et al. )] TJ ET
0.267 0.267 0.267 rg
BT 198.144 240.850 Td /F1 9.8 Tf  [([9])] TJ ET
0.271 0.267 0.267 rg
BT 149.375 233.219 Td /F1 9.8 Tf  [(Price et al. )] TJ ET
0.267 0.267 0.267 rg
BT 198.144 233.219 Td /F1 9.8 Tf  [([10])] TJ ET
0.000 0.000 0.000 rg
339.875 256.705 110.750 1.000 re f
0.267 0.267 0.267 rg
339.875 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 346.625 240.850 Td /F1 9.8 Tf  [(AA )] TJ ET
BT 346.625 233.219 Td /F1 9.8 Tf  [(NA)] TJ ET
0.000 0.000 0.000 rg
449.875 256.705 112.500 1.000 re f
0.267 0.267 0.267 rg
449.875 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 456.625 240.850 Td /F1 9.8 Tf  [(250; 1,250; )] TJ ET
BT 456.625 233.219 Td /F1 9.8 Tf  [(5,00078,132)] TJ ET
0.000 0.000 0.000 rg
561.625 256.705 110.750 1.000 re f
0.267 0.267 0.267 rg
561.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 568.375 240.850 Td /F1 9.8 Tf  [(N/A)] TJ ET
0.000 0.000 0.000 rg
671.625 256.705 193.500 1.000 re f
0.267 0.267 0.267 rg
671.625 224.292 0.750 33.413 re f
864.375 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 678.375 240.850 Td /F1 9.8 Tf  [(Rose )] TJ ET
0.267 0.267 0.267 rg
BT 703.842 240.850 Td /F1 9.8 Tf  [([11])] TJ ET
32.625 224.292 110.750 0.750 re f
32.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 39.375 208.437 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
142.625 224.292 198.000 0.750 re f
142.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 149.375 208.437 Td /F1 9.8 Tf  [(Liu et al. )] TJ ET
0.267 0.267 0.267 rg
BT 188.940 208.437 Td /F1 9.8 Tf  [([5])] TJ ET
339.875 224.292 110.750 0.750 re f
339.875 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 346.625 208.437 Td /F1 9.8 Tf  [(NA)] TJ ET
0.267 0.267 0.267 rg
449.875 224.292 112.500 0.750 re f
449.875 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 456.625 208.437 Td /F1 9.8 Tf  [(100; 500; 1,000)] TJ ET
0.267 0.267 0.267 rg
561.625 224.292 110.750 0.750 re f
561.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 568.375 208.437 Td /F1 9.8 Tf  [(1,000)] TJ ET
0.267 0.267 0.267 rg
671.625 224.292 193.500 0.750 re f
671.625 199.511 0.750 25.531 re f
864.375 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 678.375 208.437 Td /F1 9.8 Tf  [(SeqGen )] TJ ET
0.267 0.267 0.267 rg
BT 716.858 208.437 Td /F1 9.8 Tf  [([12])] TJ ET
0.271 0.267 0.267 rg
BT 733.121 208.437 Td /F1 9.8 Tf  [( Rose )] TJ ET
0.267 0.267 0.267 rg
BT 761.299 208.437 Td /F1 9.8 Tf  [([11])] TJ ET
32.625 199.511 110.375 0.750 re f
32.625 159.592 0.750 40.669 re f
0.271 0.267 0.267 rg
BT 39.000 184.031 Td /F1 9.8 Tf  [(RNASim)] TJ ET
0.267 0.267 0.267 rg
143.000 199.511 197.250 0.750 re f
BT 149.000 184.031 Td /F1 9.8 Tf  [(kim.bio.upenn.edu/software/csd.shtml)] TJ ET
340.250 199.511 110.000 0.750 re f
0.271 0.267 0.267 rg
BT 346.250 184.031 Td /F1 9.8 Tf  [(NA \(SSU rRNA\))] TJ ET
0.267 0.267 0.267 rg
450.250 199.511 111.750 0.750 re f
0.271 0.267 0.267 rg
BT 456.250 184.031 Td /F1 9.8 Tf  [(128; 256; 512; 1,024; )] TJ ET
BT 456.250 176.400 Td /F1 9.8 Tf  [(2,048; 4,096; 8,192; )] TJ ET
BT 456.250 168.769 Td /F1 9.8 Tf  [(16,384; 1,000,000)] TJ ET
0.267 0.267 0.267 rg
562.000 199.511 110.000 0.750 re f
0.271 0.267 0.267 rg
BT 568.000 184.031 Td /F1 9.8 Tf  [(1,542)] TJ ET
0.267 0.267 0.267 rg
672.000 199.511 193.125 0.750 re f
864.375 159.592 0.750 40.669 re f
0.271 0.267 0.267 rg
BT 678.000 184.031 Td /F1 9.8 Tf  [(RNASim )] TJ ET
0.267 0.267 0.267 rg
BT 718.082 184.031 Td /F1 9.8 Tf  [([13])] TJ ET
0.000 0.000 0.000 rg
32.625 159.592 110.375 1.000 re f
0.267 0.267 0.267 rg
32.625 121.278 110.375 0.750 re f
0.000 0.000 0.000 rg
143.000 159.592 197.250 1.000 re f
0.267 0.267 0.267 rg
143.000 121.278 197.250 0.750 re f
0.000 0.000 0.000 rg
340.250 159.592 110.000 1.000 re f
0.267 0.267 0.267 rg
340.250 121.278 110.000 0.750 re f
0.000 0.000 0.000 rg
450.250 159.592 111.750 1.000 re f
0.267 0.267 0.267 rg
450.250 121.278 111.750 0.750 re f
0.000 0.000 0.000 rg
562.000 159.592 110.000 1.000 re f
0.267 0.267 0.267 rg
562.000 121.278 110.000 0.750 re f
0.000 0.000 0.000 rg
672.000 159.592 193.125 1.000 re f
0.267 0.267 0.267 rg
672.000 121.278 193.125 0.750 re f
32.625 121.278 0.750 39.314 re f
864.375 121.278 0.750 39.314 re f
0.271 0.267 0.267 rg
BT 39.375 143.942 Td /F1 8.7 Tf  [(a)] TJ ET
BT 44.194 141.377 Td /F1 9.8 Tf  [( AA = amino acid; NA = nucleic acid)] TJ ET
BT 199.180 143.942 Td /F1 8.7 Tf  [(b)] TJ ET
BT 203.998 141.377 Td /F1 9.8 Tf  [( The number of characters in the root sequence)] TJ ET
BT 39.375 133.360 Td /F1 8.7 Tf  [(c)] TJ ET
BT 43.708 130.795 Td /F1 9.8 Tf  [( The software used to generate the datasets)] TJ ET
BT 26.250 56.682 Td /F4 12.0 Tf  [(Benchmarks for multiple sequence alignment)] TJ ET
BT 26.250 36.727 Td /F1 9.8 Tf  [(Most of the benchmark datasets for multiple sequence alignment are the same as those for phylogenetic estimation. Both )] TJ ET
Q
q
15.000 22.442 577.500 754.558 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(both nucleic acid and amino acid sequence data.)] TJ ET
1.000 1.000 1.000 rg
32.250 386.409 691.500 371.187 re f
0.267 0.267 0.267 rg
32.625 756.470 94.125 0.750 re f
126.750 756.470 84.750 0.750 re f
211.500 756.470 174.750 0.750 re f
386.250 756.470 84.000 0.750 re f
470.250 756.470 84.000 0.750 re f
554.250 756.470 84.000 0.750 re f
638.250 756.470 85.125 0.750 re f
32.625 731.814 0.750 25.406 re f
722.625 731.814 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 39.000 740.990 Td /F4 9.8 Tf  [(Table 1)] TJ ET
BT 72.599 740.990 Td /F1 9.8 Tf  [( . Empirical datasets and their properties.)] TJ ET
0.000 0.000 0.000 rg
32.625 731.814 94.125 1.000 re f
0.267 0.267 0.267 rg
32.625 696.701 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 39.000 714.098 Td /F4 9.8 Tf  [(Dataset)] TJ ET
BT 74.217 716.664 Td /F4 8.7 Tf  [(a)] TJ ET
0.000 0.000 0.000 rg
126.750 731.814 84.750 1.000 re f
0.271 0.267 0.267 rg
BT 132.750 716.459 Td /F4 9.8 Tf  [(Gene)] TJ ET
0.000 0.000 0.000 rg
211.500 731.814 174.750 1.000 re f
0.271 0.267 0.267 rg
BT 217.500 716.459 Td /F4 9.8 Tf  [(Taxonomic Range)] TJ ET
0.000 0.000 0.000 rg
386.250 731.814 84.000 1.000 re f
0.271 0.267 0.267 rg
BT 392.250 716.459 Td /F4 9.8 Tf  [(Number of )] TJ ET
BT 392.250 708.828 Td /F4 9.8 Tf  [(Taxa)] TJ ET
0.000 0.000 0.000 rg
470.250 731.814 84.000 1.000 re f
0.271 0.267 0.267 rg
BT 476.250 716.459 Td /F4 9.8 Tf  [(Number of )] TJ ET
BT 476.250 706.467 Td /F4 9.8 Tf  [(Characters)] TJ ET
BT 527.184 709.032 Td /F4 8.7 Tf  [(b)] TJ ET
0.000 0.000 0.000 rg
554.250 731.814 84.000 1.000 re f
0.271 0.267 0.267 rg
BT 560.250 716.459 Td /F4 9.8 Tf  [(Percentage )] TJ ET
BT 560.250 708.828 Td /F4 9.8 Tf  [(Indels)] TJ ET
0.000 0.000 0.000 rg
638.250 731.814 85.125 1.000 re f
0.267 0.267 0.267 rg
722.625 696.701 0.750 36.113 re f
0.271 0.267 0.267 rg
BT 644.250 716.459 Td /F4 9.8 Tf  [(Average Gap )] TJ ET
BT 644.250 708.828 Td /F4 9.8 Tf  [(Length)] TJ ET
0.000 0.000 0.000 rg
32.625 696.701 94.500 1.000 re f
0.267 0.267 0.267 rg
32.625 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 39.375 680.846 Td /F1 9.8 Tf  [(16S.B.ALL)] TJ ET
0.000 0.000 0.000 rg
126.375 696.701 85.500 1.000 re f
0.267 0.267 0.267 rg
126.375 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 133.125 680.846 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.000 0.000 0.000 rg
211.125 696.701 175.500 1.000 re f
0.267 0.267 0.267 rg
211.125 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 217.875 680.846 Td /F1 9.8 Tf  [(Bacteria)] TJ ET
0.000 0.000 0.000 rg
385.875 696.701 84.750 1.000 re f
0.267 0.267 0.267 rg
385.875 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 392.625 680.846 Td /F1 9.8 Tf  [(27,643)] TJ ET
0.000 0.000 0.000 rg
469.875 696.701 84.750 1.000 re f
0.267 0.267 0.267 rg
469.875 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 476.625 680.846 Td /F1 9.8 Tf  [(6,857)] TJ ET
0.000 0.000 0.000 rg
553.875 696.701 84.750 1.000 re f
0.267 0.267 0.267 rg
553.875 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 560.625 680.846 Td /F1 9.8 Tf  [(80.0)] TJ ET
0.000 0.000 0.000 rg
637.875 696.701 85.500 1.000 re f
0.267 0.267 0.267 rg
637.875 671.919 0.750 25.781 re f
722.625 671.919 0.750 25.781 re f
0.271 0.267 0.267 rg
BT 644.625 680.846 Td /F1 9.8 Tf  [(4.9)] TJ ET
0.267 0.267 0.267 rg
32.625 671.919 94.500 0.750 re f
32.625 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 39.375 656.065 Td /F1 9.8 Tf  [(16S.T)] TJ ET
0.267 0.267 0.267 rg
126.375 671.919 85.500 0.750 re f
126.375 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 133.125 656.065 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 671.919 175.500 0.750 re f
211.125 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 217.875 656.065 Td /F1 9.8 Tf  [(The three domains of life plus )] TJ ET
BT 217.875 648.433 Td /F1 9.8 Tf  [(mitochondria and chloroplasts)] TJ ET
0.267 0.267 0.267 rg
385.875 671.919 84.750 0.750 re f
385.875 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 392.625 656.065 Td /F1 9.8 Tf  [(7,350)] TJ ET
0.267 0.267 0.267 rg
469.875 671.919 84.750 0.750 re f
469.875 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 476.625 656.065 Td /F1 9.8 Tf  [(11,856)] TJ ET
0.267 0.267 0.267 rg
553.875 671.919 84.750 0.750 re f
553.875 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 560.625 656.065 Td /F1 9.8 Tf  [(87.4)] TJ ET
0.267 0.267 0.267 rg
637.875 671.919 85.500 0.750 re f
637.875 639.507 0.750 33.162 re f
722.625 639.507 0.750 33.162 re f
0.271 0.267 0.267 rg
BT 644.625 656.065 Td /F1 9.8 Tf  [(12.1)] TJ ET
0.267 0.267 0.267 rg
32.625 639.507 94.500 0.750 re f
32.625 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 39.375 623.652 Td /F1 9.8 Tf  [(16S.3)] TJ ET
0.267 0.267 0.267 rg
126.375 639.507 85.500 0.750 re f
126.375 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 133.125 623.652 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 639.507 175.500 0.750 re f
211.125 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 217.875 623.652 Td /F1 9.8 Tf  [(The three domains of life)] TJ ET
0.267 0.267 0.267 rg
385.875 639.507 84.750 0.750 re f
385.875 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 392.625 623.652 Td /F1 9.8 Tf  [(6,323)] TJ ET
0.267 0.267 0.267 rg
469.875 639.507 84.750 0.750 re f
469.875 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 476.625 623.652 Td /F1 9.8 Tf  [(8,716)] TJ ET
0.267 0.267 0.267 rg
553.875 639.507 84.750 0.750 re f
553.875 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 560.625 623.652 Td /F1 9.8 Tf  [(82.1)] TJ ET
0.267 0.267 0.267 rg
637.875 639.507 85.500 0.750 re f
637.875 614.726 0.750 25.531 re f
722.625 614.726 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 644.625 623.652 Td /F1 9.8 Tf  [(9.4)] TJ ET
0.267 0.267 0.267 rg
32.625 614.726 94.500 0.750 re f
32.625 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 39.375 596.510 Td /F1 9.8 Tf  [(16S.M.aa_ag )] TJ ET
BT 100.078 599.075 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
126.375 614.726 85.500 0.750 re f
126.375 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 133.125 598.871 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 614.726 175.500 0.750 re f
211.125 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 217.875 598.871 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 614.726 84.750 0.750 re f
385.875 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 392.625 598.871 Td /F1 9.8 Tf  [(1,028)] TJ ET
0.267 0.267 0.267 rg
469.875 614.726 84.750 0.750 re f
469.875 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 476.625 598.871 Td /F1 9.8 Tf  [(4,907)] TJ ET
0.267 0.267 0.267 rg
553.875 614.726 84.750 0.750 re f
553.875 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 560.625 598.871 Td /F1 9.8 Tf  [(82.6)] TJ ET
0.267 0.267 0.267 rg
637.875 614.726 85.500 0.750 re f
637.875 586.994 0.750 28.482 re f
722.625 586.994 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 644.625 598.871 Td /F1 9.8 Tf  [(22.0)] TJ ET
0.267 0.267 0.267 rg
32.625 586.994 94.500 0.750 re f
32.625 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 39.375 571.139 Td /F1 9.8 Tf  [(16S.M)] TJ ET
0.267 0.267 0.267 rg
126.375 586.994 85.500 0.750 re f
126.375 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 133.125 571.139 Td /F1 9.8 Tf  [(16S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 586.994 175.500 0.750 re f
211.125 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 217.875 571.139 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 586.994 84.750 0.750 re f
385.875 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 392.625 571.139 Td /F1 9.8 Tf  [(901)] TJ ET
0.267 0.267 0.267 rg
469.875 586.994 84.750 0.750 re f
469.875 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 476.625 571.139 Td /F1 9.8 Tf  [(4,722)] TJ ET
0.267 0.267 0.267 rg
553.875 586.994 84.750 0.750 re f
553.875 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 560.625 571.139 Td /F1 9.8 Tf  [(78.1)] TJ ET
0.267 0.267 0.267 rg
637.875 586.994 85.500 0.750 re f
637.875 555.844 0.750 31.900 re f
722.625 555.844 0.750 31.900 re f
0.271 0.267 0.267 rg
BT 644.625 571.139 Td /F1 9.8 Tf  [(17.2)] TJ ET
0.267 0.267 0.267 rg
32.625 555.844 94.500 0.750 re f
32.625 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 39.375 539.989 Td /F1 9.8 Tf  [(23S.M)] TJ ET
0.267 0.267 0.267 rg
126.375 555.844 85.500 0.750 re f
126.375 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 133.125 539.989 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 555.844 175.500 0.750 re f
211.125 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 217.875 539.989 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 555.844 84.750 0.750 re f
385.875 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 392.625 539.989 Td /F1 9.8 Tf  [(278)] TJ ET
0.267 0.267 0.267 rg
469.875 555.844 84.750 0.750 re f
469.875 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 476.625 539.989 Td /F1 9.8 Tf  [(10,738)] TJ ET
0.267 0.267 0.267 rg
553.875 555.844 84.750 0.750 re f
553.875 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 560.625 539.989 Td /F1 9.8 Tf  [(83.7)] TJ ET
0.267 0.267 0.267 rg
637.875 555.844 85.500 0.750 re f
637.875 531.062 0.750 25.531 re f
722.625 531.062 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 644.625 539.989 Td /F1 9.8 Tf  [(31.9)] TJ ET
0.267 0.267 0.267 rg
32.625 531.062 94.500 0.750 re f
32.625 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 39.375 512.847 Td /F1 9.8 Tf  [(23S.M.aa_ag )] TJ ET
BT 100.078 515.412 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
126.375 531.062 85.500 0.750 re f
126.375 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 133.125 515.207 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 531.062 175.500 0.750 re f
211.125 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 217.875 515.207 Td /F1 9.8 Tf  [(Mitochondria)] TJ ET
0.267 0.267 0.267 rg
385.875 531.062 84.750 0.750 re f
385.875 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 392.625 515.207 Td /F1 9.8 Tf  [(263)] TJ ET
0.267 0.267 0.267 rg
469.875 531.062 84.750 0.750 re f
469.875 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 476.625 515.207 Td /F1 9.8 Tf  [(10,305)] TJ ET
0.267 0.267 0.267 rg
553.875 531.062 84.750 0.750 re f
553.875 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 560.625 515.207 Td /F1 9.8 Tf  [(83.5)] TJ ET
0.267 0.267 0.267 rg
637.875 531.062 85.500 0.750 re f
637.875 503.331 0.750 28.482 re f
722.625 503.331 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 644.625 515.207 Td /F1 9.8 Tf  [(34.2)] TJ ET
0.267 0.267 0.267 rg
32.625 503.331 94.500 0.750 re f
32.625 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 39.375 485.115 Td /F1 9.8 Tf  [(23S.E.aa_ag )] TJ ET
BT 98.460 487.680 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
126.375 503.331 85.500 0.750 re f
126.375 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 133.125 487.476 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.125 503.331 175.500 0.750 re f
211.125 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 217.875 487.476 Td /F1 9.8 Tf  [(Eukaryotes nuclear)] TJ ET
0.267 0.267 0.267 rg
385.875 503.331 84.750 0.750 re f
385.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 392.625 487.476 Td /F1 9.8 Tf  [(144)] TJ ET
0.267 0.267 0.267 rg
469.875 503.331 84.750 0.750 re f
469.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 476.625 487.476 Td /F1 9.8 Tf  [(8,619)] TJ ET
0.267 0.267 0.267 rg
553.875 503.331 84.750 0.750 re f
553.875 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 560.625 487.476 Td /F1 9.8 Tf  [(61.1)] TJ ET
0.267 0.267 0.267 rg
637.875 503.331 85.500 0.750 re f
637.875 475.599 0.750 28.482 re f
722.625 475.599 0.750 28.482 re f
0.271 0.267 0.267 rg
BT 644.625 487.476 Td /F1 9.8 Tf  [(13.5)] TJ ET
0.267 0.267 0.267 rg
32.625 475.599 94.125 0.750 re f
32.625 450.942 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 39.000 460.119 Td /F1 9.8 Tf  [(23S.E)] TJ ET
0.267 0.267 0.267 rg
126.750 475.599 84.750 0.750 re f
0.271 0.267 0.267 rg
BT 132.750 460.119 Td /F1 9.8 Tf  [(23S rRNA)] TJ ET
0.267 0.267 0.267 rg
211.500 475.599 174.750 0.750 re f
0.271 0.267 0.267 rg
BT 217.500 460.119 Td /F1 9.8 Tf  [(Eukaryotes)] TJ ET
0.267 0.267 0.267 rg
386.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 392.250 460.119 Td /F1 9.8 Tf  [(117)] TJ ET
0.267 0.267 0.267 rg
470.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 476.250 460.119 Td /F1 9.8 Tf  [(9,079)] TJ ET
0.267 0.267 0.267 rg
554.250 475.599 84.000 0.750 re f
0.271 0.267 0.267 rg
BT 560.250 460.119 Td /F1 9.8 Tf  [(59.7)] TJ ET
0.267 0.267 0.267 rg
638.250 475.599 85.125 0.750 re f
722.625 450.942 0.750 25.406 re f
0.271 0.267 0.267 rg
BT 644.250 460.119 Td /F1 9.8 Tf  [(12.6)] TJ ET
0.000 0.000 0.000 rg
32.625 450.942 94.125 1.000 re f
0.267 0.267 0.267 rg
32.625 386.784 94.125 0.750 re f
0.000 0.000 0.000 rg
126.750 450.942 84.750 1.000 re f
0.267 0.267 0.267 rg
126.750 386.784 84.750 0.750 re f
0.000 0.000 0.000 rg
211.500 450.942 174.750 1.000 re f
0.267 0.267 0.267 rg
211.500 386.784 174.750 0.750 re f
0.000 0.000 0.000 rg
386.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
386.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
470.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
470.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
554.250 450.942 84.000 1.000 re f
0.267 0.267 0.267 rg
554.250 386.784 84.000 0.750 re f
0.000 0.000 0.000 rg
638.250 450.942 85.125 1.000 re f
0.267 0.267 0.267 rg
638.250 386.784 85.125 0.750 re f
32.625 386.784 0.750 65.159 re f
722.625 386.784 0.750 65.159 re f
0.271 0.267 0.267 rg
BT 39.375 435.292 Td /F1 8.7 Tf  [(a)] TJ ET
BT 44.194 432.727 Td /F1 9.8 Tf  [( Unless otherwise noted, all datasets in this table are taken from Cannone et al. )] TJ ET
0.267 0.267 0.267 rg
BT 389.402 432.727 Td /F1 9.8 Tf  [([7])] TJ ET
0.271 0.267 0.267 rg
BT 400.244 432.727 Td /F1 9.8 Tf  [(. Curated alignments were produced by Cannone et al. using covariation )] TJ ET
BT 39.375 424.505 Td /F1 9.8 Tf  [(and secondary structure. The reference trees reported on our web site were generated using RAxML version 7.0.4. Complete run parameters and program )] TJ ET
BT 39.375 416.874 Td /F1 9.8 Tf  [(commands are listed on the web site.)] TJ ET
BT 39.375 409.447 Td /F1 8.7 Tf  [(b)] TJ ET
BT 44.194 406.882 Td /F1 9.8 Tf  [( The number of columns in the aligned dataset. )] TJ ET
BT 39.375 398.865 Td /F1 8.7 Tf  [(c)] TJ ET
0.267 0.267 0.267 rg
BT 43.708 396.300 Td /F1 9.8 Tf  [([8])] TJ ET
0.271 0.267 0.267 rg
BT 26.250 339.385 Td /F1 9.8 Tf  [(Simulated datasets \(Table 2\) were taken from three sources and include both amino acid and nucleil acid sequences of widely )] TJ ET
BT 26.250 327.480 Td /F1 9.8 Tf  [(varying numbers of sequences, rates of substitution and sizes and rates of indels.)] TJ ET
1.000 1.000 1.000 rg
32.250 120.903 833.250 196.696 re f
0.267 0.267 0.267 rg
32.625 316.474 110.375 0.750 re f
143.000 316.474 197.250 0.750 re f
340.250 316.474 110.000 0.750 re f
450.250 316.474 111.750 0.750 re f
562.000 316.474 110.000 0.750 re f
672.000 316.474 193.125 0.750 re f
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864.375 291.818 0.750 25.406 re f
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562.000 291.818 110.000 1.000 re f
0.271 0.267 0.267 rg
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864.375 256.705 0.750 36.113 re f
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142.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
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0.271 0.267 0.267 rg
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0.267 0.267 0.267 rg
339.875 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
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0.267 0.267 0.267 rg
449.875 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 456.625 240.850 Td /F1 9.8 Tf  [(250; 1,250; )] TJ ET
BT 456.625 233.219 Td /F1 9.8 Tf  [(5,00078,132)] TJ ET
0.000 0.000 0.000 rg
561.625 256.705 110.750 1.000 re f
0.267 0.267 0.267 rg
561.625 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
BT 568.375 240.850 Td /F1 9.8 Tf  [(N/A)] TJ ET
0.000 0.000 0.000 rg
671.625 256.705 193.500 1.000 re f
0.267 0.267 0.267 rg
671.625 224.292 0.750 33.413 re f
864.375 224.292 0.750 33.413 re f
0.271 0.267 0.267 rg
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0.267 0.267 0.267 rg
BT 703.842 240.850 Td /F1 9.8 Tf  [([11])] TJ ET
32.625 224.292 110.750 0.750 re f
32.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 39.375 208.437 Td /F1 9.8 Tf  [(SAT�)] TJ ET
0.267 0.267 0.267 rg
142.625 224.292 198.000 0.750 re f
142.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 149.375 208.437 Td /F1 9.8 Tf  [(Liu et al. )] TJ ET
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BT 188.940 208.437 Td /F1 9.8 Tf  [([5])] TJ ET
339.875 224.292 110.750 0.750 re f
339.875 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
BT 346.625 208.437 Td /F1 9.8 Tf  [(NA)] TJ ET
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449.875 224.292 112.500 0.750 re f
449.875 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
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0.267 0.267 0.267 rg
561.625 224.292 110.750 0.750 re f
561.625 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
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671.625 224.292 193.500 0.750 re f
671.625 199.511 0.750 25.531 re f
864.375 199.511 0.750 25.531 re f
0.271 0.267 0.267 rg
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32.625 159.592 0.750 40.669 re f
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BT 346.250 184.031 Td /F1 9.8 Tf  [(NA \(SSU rRNA\))] TJ ET
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450.250 199.511 111.750 0.750 re f
0.271 0.267 0.267 rg
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562.000 199.511 110.000 0.750 re f
0.271 0.267 0.267 rg
BT 568.000 184.031 Td /F1 9.8 Tf  [(1,542)] TJ ET
0.267 0.267 0.267 rg
672.000 199.511 193.125 0.750 re f
864.375 159.592 0.750 40.669 re f
0.271 0.267 0.267 rg
BT 678.000 184.031 Td /F1 9.8 Tf  [(RNASim )] TJ ET
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BT 718.082 184.031 Td /F1 9.8 Tf  [([13])] TJ ET
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0.267 0.267 0.267 rg
32.625 121.278 110.375 0.750 re f
0.000 0.000 0.000 rg
143.000 159.592 197.250 1.000 re f
0.267 0.267 0.267 rg
143.000 121.278 197.250 0.750 re f
0.000 0.000 0.000 rg
340.250 159.592 110.000 1.000 re f
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340.250 121.278 110.000 0.750 re f
0.000 0.000 0.000 rg
450.250 159.592 111.750 1.000 re f
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450.250 121.278 111.750 0.750 re f
0.000 0.000 0.000 rg
562.000 159.592 110.000 1.000 re f
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562.000 121.278 110.000 0.750 re f
0.000 0.000 0.000 rg
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672.000 121.278 193.125 0.750 re f
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BT 26.250 755.571 Td /F1 9.8 Tf  [(markers currently used in large-scale phylogeny estimation and of markers that have evolved under high rates of indels, and are )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(thus extremely difficult to align.)] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(In addition to the simulated datasets for phylogeny estimation, a simulated amino acid dataset is included )] TJ ET
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0.000 0.000 0.000 rg
182.349 538.205 170.980 1.000 re f
0.271 0.267 0.267 rg
BT 188.349 528.850 Td /F4 9.8 Tf  [(Taxonomic Range)] TJ ET
0.000 0.000 0.000 rg
353.329 538.205 91.240 1.000 re f
0.271 0.267 0.267 rg
BT 359.329 528.850 Td /F4 9.8 Tf  [(Total Taxa)] TJ ET
0.000 0.000 0.000 rg
444.570 538.205 136.305 1.000 re f
0.267 0.267 0.267 rg
580.125 522.574 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.570 528.850 Td /F4 9.8 Tf  [(Number of Source Trees)] TJ ET
0.000 0.000 0.000 rg
26.625 522.574 156.099 1.000 re f
0.267 0.267 0.267 rg
26.625 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 33.375 512.719 Td /F1 9.8 Tf  [(McMahon and Sanderson )] TJ ET
0.267 0.267 0.267 rg
BT 147.723 512.719 Td /F1 9.8 Tf  [([21])] TJ ET
0.000 0.000 0.000 rg
181.974 522.574 171.730 1.000 re f
0.267 0.267 0.267 rg
181.974 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 188.724 512.719 Td /F1 9.8 Tf  [(Comprehensive papilionoid legumes)] TJ ET
0.000 0.000 0.000 rg
352.954 522.574 91.990 1.000 re f
0.267 0.267 0.267 rg
352.954 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 359.704 512.719 Td /F1 9.8 Tf  [(2,228)] TJ ET
0.000 0.000 0.000 rg
444.195 522.574 136.680 1.000 re f
0.267 0.267 0.267 rg
444.195 506.692 0.750 16.881 re f
580.125 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 450.945 512.719 Td /F1 9.8 Tf  [(39)] TJ ET
0.267 0.267 0.267 rg
26.625 506.692 156.099 0.750 re f
26.625 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 496.837 Td /F1 9.8 Tf  [(Cardillo et al. )] TJ ET
0.267 0.267 0.267 rg
BT 92.977 496.837 Td /F1 9.8 Tf  [([22])] TJ ET
181.974 506.692 171.730 0.750 re f
181.974 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 496.837 Td /F1 9.8 Tf  [(Marsupials)] TJ ET
0.267 0.267 0.267 rg
352.954 506.692 91.990 0.750 re f
352.954 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 496.837 Td /F1 9.8 Tf  [(267)] TJ ET
0.267 0.267 0.267 rg
444.195 506.692 136.680 0.750 re f
444.195 490.811 0.750 16.631 re f
580.125 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 496.837 Td /F1 9.8 Tf  [(158)] TJ ET
0.267 0.267 0.267 rg
26.625 490.811 156.099 0.750 re f
26.625 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 480.956 Td /F1 9.8 Tf  [(Beck et al. )] TJ ET
0.267 0.267 0.267 rg
BT 81.608 480.956 Td /F1 9.8 Tf  [([23])] TJ ET
181.974 490.811 171.730 0.750 re f
181.974 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 480.956 Td /F1 9.8 Tf  [(Placental mammals)] TJ ET
0.267 0.267 0.267 rg
352.954 490.811 91.990 0.750 re f
352.954 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 480.956 Td /F1 9.8 Tf  [(116)] TJ ET
0.267 0.267 0.267 rg
444.195 490.811 136.680 0.750 re f
444.195 474.930 0.750 16.631 re f
580.125 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 480.956 Td /F1 9.8 Tf  [(726)] TJ ET
0.267 0.267 0.267 rg
26.625 474.930 156.099 0.750 re f
26.625 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 465.075 Td /F1 9.8 Tf  [(Kennedy and Page )] TJ ET
0.267 0.267 0.267 rg
BT 119.019 465.075 Td /F1 9.8 Tf  [([24])] TJ ET
181.974 474.930 171.730 0.750 re f
181.974 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 465.075 Td /F1 9.8 Tf  [(Seabirds)] TJ ET
0.267 0.267 0.267 rg
352.954 474.930 91.990 0.750 re f
352.954 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 465.075 Td /F1 9.8 Tf  [(121)] TJ ET
0.267 0.267 0.267 rg
444.195 474.930 136.680 0.750 re f
444.195 459.049 0.750 16.631 re f
580.125 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 465.075 Td /F1 9.8 Tf  [(7)] TJ ET
0.267 0.267 0.267 rg
26.625 459.049 155.724 0.750 re f
0.000 0.000 0.000 rg
26.625 435.661 155.724 1.000 re f
0.267 0.267 0.267 rg
26.625 435.661 0.750 24.138 re f
0.271 0.267 0.267 rg
BT 33.000 442.069 Td /F1 9.8 Tf  [(Wojciechowski et al. )] TJ ET
0.267 0.267 0.267 rg
BT 123.480 442.069 Td /F1 9.8 Tf  [([25])] TJ ET
182.349 459.049 170.980 0.750 re f
0.000 0.000 0.000 rg
182.349 435.661 170.980 1.000 re f
0.271 0.267 0.267 rg
BT 188.349 449.569 Td /F1 9.8 Tf  [(Temperate herbaceous papilionoid )] TJ ET
BT 188.349 441.937 Td /F1 9.8 Tf  [(legumes)] TJ ET
0.267 0.267 0.267 rg
353.329 459.049 91.240 0.750 re f
0.000 0.000 0.000 rg
353.329 435.661 91.240 1.000 re f
0.271 0.267 0.267 rg
BT 359.329 449.569 Td /F1 9.8 Tf  [(558)] TJ ET
0.267 0.267 0.267 rg
444.570 459.049 136.305 0.750 re f
0.000 0.000 0.000 rg
444.570 435.661 136.305 1.000 re f
0.267 0.267 0.267 rg
580.125 435.661 0.750 24.138 re f
0.271 0.267 0.267 rg
BT 450.570 449.569 Td /F1 9.8 Tf  [(19)] TJ ET
BT 26.250 371.190 Td /F4 12.0 Tf  [(Software for generating datasets)] TJ ET
BT 26.250 351.235 Td /F1 9.8 Tf  [(The collection of simulation software is useful for three aspects of producing simulated datasets: generating simulated )] TJ ET
BT 26.250 339.331 Td /F1 9.8 Tf  [(phylogenetic trees \(e.g., r8s )] TJ ET
0.267 0.267 0.267 rg
BT 149.266 339.331 Td /F1 9.8 Tf  [([26])] TJ ET
0.271 0.267 0.267 rg
BT 165.529 339.331 Td /F1 9.8 Tf  [( and Mesquite )] TJ ET
0.267 0.267 0.267 rg
BT 229.479 339.331 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 245.742 339.331 Td /F1 9.8 Tf  [(\); evolving sequences on phylogenetic trees \(particularly tools that evolve )] TJ ET
BT 26.250 327.426 Td /F1 9.8 Tf  [(sequences with both substitution and indel events\) and tools for post-processing model trees in order to deviate from the model )] TJ ET
BT 26.250 315.521 Td /F1 9.8 Tf  [(assumptions \(such as the molecular clock\).)] TJ ET
BT 26.250 278.919 Td /F4 12.0 Tf  [(Conclusions)] TJ ET
BT 26.250 258.964 Td /F1 9.8 Tf  [(We hope that having these benchmark datasets in a single location will facilitate research on large-scale phylogenetic methods )] TJ ET
BT 26.250 247.060 Td /F1 9.8 Tf  [(and enhance the reproducibility of work based upon the datasets. We also hope that posting simulation tools that are capable of )] TJ ET
BT 26.250 235.155 Td /F1 9.8 Tf  [(generating large-scale phylogenetic datasets will promote the generation of new benchmark datasets for use by the community.)] TJ ET
BT 26.250 215.750 Td /F1 9.8 Tf  [(We conceive of these pages as an evolving resource for the community and welcome input that would improve or expand them. )] TJ ET
BT 26.250 203.845 Td /F1 9.8 Tf  [(We invite readers to contact us if they wish to contribute benchmark datasets or software to this resource or if they know of )] TJ ET
BT 26.250 191.941 Td /F1 9.8 Tf  [(additional datasets or software that should be added to the pages. We will be happy to work with the laboratories providing )] TJ ET
BT 26.250 180.036 Td /F1 9.8 Tf  [(them, and will either store them locally or provide links to their sites.)] TJ ET
BT 26.250 143.433 Td /F4 12.0 Tf  [(Competing Interests)] TJ ET
BT 26.250 123.479 Td /F1 9.8 Tf  [(The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 86.877 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 66.922 Td /F1 9.8 Tf  [(The authors thank the editors and two anonymous reviewers for their very helpful suggestions on the manuscript. )] TJ ET
BT 26.250 55.018 Td /F1 9.8 Tf  [(Correspondence should be sent to CRL. The research was supported by the US National Science Foundation DEB 0733029, )] TJ ET
BT 26.250 43.113 Td /F1 9.8 Tf  [(and by Microsoft Research through support to TW.)] TJ ET
Q
q
15.000 40.732 577.500 736.268 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(empirical and simulated datasets are provided. Taken as a whole, these datasets have properties that are typical both of )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(markers currently used in large-scale phylogeny estimation and of markers that have evolved under high rates of indels, and are )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(thus extremely difficult to align.)] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(In addition to the simulated datasets for phylogeny estimation, a simulated amino acid dataset is included )] TJ ET
0.267 0.267 0.267 rg
BT 482.014 724.262 Td /F1 9.8 Tf  [([14])] TJ ET
0.271 0.267 0.267 rg
BT 498.277 724.262 Td /F1 9.8 Tf  [(, which has )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(sequences that were generated using Rose )] TJ ET
0.267 0.267 0.267 rg
BT 217.018 712.357 Td /F1 9.8 Tf  [([11])] TJ ET
0.271 0.267 0.267 rg
BT 233.281 712.357 Td /F1 9.8 Tf  [( and ranging from 20 to 100 taxa. Several additional empirical amino acid )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(datasets are also included \(BAliBASE )] TJ ET
0.267 0.267 0.267 rg
BT 191.532 700.452 Td /F1 9.8 Tf  [([15])] TJ ET
0.271 0.267 0.267 rg
BT 207.795 700.452 Td /F1 9.8 Tf  [(, OXBench )] TJ ET
0.267 0.267 0.267 rg
BT 257.657 700.452 Td /F1 9.8 Tf  [([16])] TJ ET
0.271 0.267 0.267 rg
BT 273.920 700.452 Td /F1 9.8 Tf  [(, PREFAB )] TJ ET
0.267 0.267 0.267 rg
BT 321.061 700.452 Td /F1 9.8 Tf  [([17])] TJ ET
0.271 0.267 0.267 rg
BT 337.324 700.452 Td /F1 9.8 Tf  [(, SABmark )] TJ ET
0.267 0.267 0.267 rg
BT 386.630 700.452 Td /F1 9.8 Tf  [([18])] TJ ET
0.271 0.267 0.267 rg
BT 402.892 700.452 Td /F1 9.8 Tf  [(\).)] TJ ET
BT 26.250 681.048 Td /F1 9.8 Tf  [(The empirical benchmark datasets for testing multiple sequence alignment include datasets with highly reliable curated )] TJ ET
BT 26.250 669.143 Td /F1 9.8 Tf  [(sequence alignments that have been carefully validated by the community. The gold standard for this sort of dataset is Robin )] TJ ET
BT 26.250 657.238 Td /F1 9.8 Tf  [(Gutell�s Comparative RNA Website \(CRW\) )] TJ ET
0.267 0.267 0.267 rg
BT 213.148 657.238 Td /F1 9.8 Tf  [([19])] TJ ET
0.271 0.267 0.267 rg
BT 229.411 657.238 Td /F1 9.8 Tf  [(. The curated alignments provided in CRW are based upon secondary structural )] TJ ET
BT 26.250 645.333 Td /F1 9.8 Tf  [(information, which is particularly helpful where the mature rRNA is double stranded due to sequence complementarity.)] TJ ET
BT 26.250 608.731 Td /F4 12.0 Tf  [(Benchmarks for supertree methods)] TJ ET
BT 26.250 588.777 Td /F1 9.8 Tf  [(Finally, we provide benchmarks for testing supertree methods. As with the other benchmark collections, we provide both )] TJ ET
BT 26.250 576.872 Td /F1 9.8 Tf  [(empirical \(Table 3\) and simulated )] TJ ET
0.267 0.267 0.267 rg
BT 173.085 576.872 Td /F1 9.8 Tf  [([20])] TJ ET
0.271 0.267 0.267 rg
BT 189.348 576.872 Td /F1 9.8 Tf  [( supertree datasets, and include datasets with different properties \(such as the number of )] TJ ET
BT 26.250 564.967 Td /F1 9.8 Tf  [(source trees, and the taxon sampling strategies used to produce the source trees\).)] TJ ET
1.000 1.000 1.000 rg
26.250 435.411 555.000 119.675 re f
0.267 0.267 0.267 rg
26.625 553.961 155.724 0.750 re f
182.349 553.961 170.980 0.750 re f
353.329 553.961 91.240 0.750 re f
444.570 553.961 136.305 0.750 re f
26.625 538.205 0.750 16.506 re f
580.125 538.205 0.750 16.506 re f
0.271 0.267 0.267 rg
BT 33.000 544.481 Td /F4 9.8 Tf  [(Table 3)] TJ ET
BT 66.599 544.481 Td /F1 9.8 Tf  [( . Empirical supertree datasets.)] TJ ET
0.000 0.000 0.000 rg
26.625 538.205 155.724 1.000 re f
0.267 0.267 0.267 rg
26.625 522.574 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.000 528.850 Td /F4 9.8 Tf  [(Dataset)] TJ ET
0.000 0.000 0.000 rg
182.349 538.205 170.980 1.000 re f
0.271 0.267 0.267 rg
BT 188.349 528.850 Td /F4 9.8 Tf  [(Taxonomic Range)] TJ ET
0.000 0.000 0.000 rg
353.329 538.205 91.240 1.000 re f
0.271 0.267 0.267 rg
BT 359.329 528.850 Td /F4 9.8 Tf  [(Total Taxa)] TJ ET
0.000 0.000 0.000 rg
444.570 538.205 136.305 1.000 re f
0.267 0.267 0.267 rg
580.125 522.574 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.570 528.850 Td /F4 9.8 Tf  [(Number of Source Trees)] TJ ET
0.000 0.000 0.000 rg
26.625 522.574 156.099 1.000 re f
0.267 0.267 0.267 rg
26.625 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 33.375 512.719 Td /F1 9.8 Tf  [(McMahon and Sanderson )] TJ ET
0.267 0.267 0.267 rg
BT 147.723 512.719 Td /F1 9.8 Tf  [([21])] TJ ET
0.000 0.000 0.000 rg
181.974 522.574 171.730 1.000 re f
0.267 0.267 0.267 rg
181.974 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 188.724 512.719 Td /F1 9.8 Tf  [(Comprehensive papilionoid legumes)] TJ ET
0.000 0.000 0.000 rg
352.954 522.574 91.990 1.000 re f
0.267 0.267 0.267 rg
352.954 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 359.704 512.719 Td /F1 9.8 Tf  [(2,228)] TJ ET
0.000 0.000 0.000 rg
444.195 522.574 136.680 1.000 re f
0.267 0.267 0.267 rg
444.195 506.692 0.750 16.881 re f
580.125 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 450.945 512.719 Td /F1 9.8 Tf  [(39)] TJ ET
0.267 0.267 0.267 rg
26.625 506.692 156.099 0.750 re f
26.625 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 496.837 Td /F1 9.8 Tf  [(Cardillo et al. )] TJ ET
0.267 0.267 0.267 rg
BT 92.977 496.837 Td /F1 9.8 Tf  [([22])] TJ ET
181.974 506.692 171.730 0.750 re f
181.974 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 496.837 Td /F1 9.8 Tf  [(Marsupials)] TJ ET
0.267 0.267 0.267 rg
352.954 506.692 91.990 0.750 re f
352.954 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 496.837 Td /F1 9.8 Tf  [(267)] TJ ET
0.267 0.267 0.267 rg
444.195 506.692 136.680 0.750 re f
444.195 490.811 0.750 16.631 re f
580.125 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 496.837 Td /F1 9.8 Tf  [(158)] TJ ET
0.267 0.267 0.267 rg
26.625 490.811 156.099 0.750 re f
26.625 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 480.956 Td /F1 9.8 Tf  [(Beck et al. )] TJ ET
0.267 0.267 0.267 rg
BT 81.608 480.956 Td /F1 9.8 Tf  [([23])] TJ ET
181.974 490.811 171.730 0.750 re f
181.974 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 480.956 Td /F1 9.8 Tf  [(Placental mammals)] TJ ET
0.267 0.267 0.267 rg
352.954 490.811 91.990 0.750 re f
352.954 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 480.956 Td /F1 9.8 Tf  [(116)] TJ ET
0.267 0.267 0.267 rg
444.195 490.811 136.680 0.750 re f
444.195 474.930 0.750 16.631 re f
580.125 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 480.956 Td /F1 9.8 Tf  [(726)] TJ ET
0.267 0.267 0.267 rg
26.625 474.930 156.099 0.750 re f
26.625 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 465.075 Td /F1 9.8 Tf  [(Kennedy and Page )] TJ ET
0.267 0.267 0.267 rg
BT 119.019 465.075 Td /F1 9.8 Tf  [([24])] TJ ET
181.974 474.930 171.730 0.750 re f
181.974 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 465.075 Td /F1 9.8 Tf  [(Seabirds)] TJ ET
0.267 0.267 0.267 rg
352.954 474.930 91.990 0.750 re f
352.954 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 465.075 Td /F1 9.8 Tf  [(121)] TJ ET
0.267 0.267 0.267 rg
444.195 474.930 136.680 0.750 re f
444.195 459.049 0.750 16.631 re f
580.125 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 465.075 Td /F1 9.8 Tf  [(7)] TJ ET
0.267 0.267 0.267 rg
26.625 459.049 155.724 0.750 re f
0.000 0.000 0.000 rg
26.625 435.661 155.724 1.000 re f
0.267 0.267 0.267 rg
26.625 435.661 0.750 24.138 re f
0.271 0.267 0.267 rg
BT 33.000 442.069 Td /F1 9.8 Tf  [(Wojciechowski et al. )] TJ ET
0.267 0.267 0.267 rg
BT 123.480 442.069 Td /F1 9.8 Tf  [([25])] TJ ET
182.349 459.049 170.980 0.750 re f
0.000 0.000 0.000 rg
182.349 435.661 170.980 1.000 re f
0.271 0.267 0.267 rg
BT 188.349 449.569 Td /F1 9.8 Tf  [(Temperate herbaceous papilionoid )] TJ ET
BT 188.349 441.937 Td /F1 9.8 Tf  [(legumes)] TJ ET
0.267 0.267 0.267 rg
353.329 459.049 91.240 0.750 re f
0.000 0.000 0.000 rg
353.329 435.661 91.240 1.000 re f
0.271 0.267 0.267 rg
BT 359.329 449.569 Td /F1 9.8 Tf  [(558)] TJ ET
0.267 0.267 0.267 rg
444.570 459.049 136.305 0.750 re f
0.000 0.000 0.000 rg
444.570 435.661 136.305 1.000 re f
0.267 0.267 0.267 rg
580.125 435.661 0.750 24.138 re f
0.271 0.267 0.267 rg
BT 450.570 449.569 Td /F1 9.8 Tf  [(19)] TJ ET
BT 26.250 371.190 Td /F4 12.0 Tf  [(Software for generating datasets)] TJ ET
BT 26.250 351.235 Td /F1 9.8 Tf  [(The collection of simulation software is useful for three aspects of producing simulated datasets: generating simulated )] TJ ET
BT 26.250 339.331 Td /F1 9.8 Tf  [(phylogenetic trees \(e.g., r8s )] TJ ET
0.267 0.267 0.267 rg
BT 149.266 339.331 Td /F1 9.8 Tf  [([26])] TJ ET
0.271 0.267 0.267 rg
BT 165.529 339.331 Td /F1 9.8 Tf  [( and Mesquite )] TJ ET
0.267 0.267 0.267 rg
BT 229.479 339.331 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 245.742 339.331 Td /F1 9.8 Tf  [(\); evolving sequences on phylogenetic trees \(particularly tools that evolve )] TJ ET
BT 26.250 327.426 Td /F1 9.8 Tf  [(sequences with both substitution and indel events\) and tools for post-processing model trees in order to deviate from the model )] TJ ET
BT 26.250 315.521 Td /F1 9.8 Tf  [(assumptions \(such as the molecular clock\).)] TJ ET
BT 26.250 278.919 Td /F4 12.0 Tf  [(Conclusions)] TJ ET
BT 26.250 258.964 Td /F1 9.8 Tf  [(We hope that having these benchmark datasets in a single location will facilitate research on large-scale phylogenetic methods )] TJ ET
BT 26.250 247.060 Td /F1 9.8 Tf  [(and enhance the reproducibility of work based upon the datasets. We also hope that posting simulation tools that are capable of )] TJ ET
BT 26.250 235.155 Td /F1 9.8 Tf  [(generating large-scale phylogenetic datasets will promote the generation of new benchmark datasets for use by the community.)] TJ ET
BT 26.250 215.750 Td /F1 9.8 Tf  [(We conceive of these pages as an evolving resource for the community and welcome input that would improve or expand them. )] TJ ET
BT 26.250 203.845 Td /F1 9.8 Tf  [(We invite readers to contact us if they wish to contribute benchmark datasets or software to this resource or if they know of )] TJ ET
BT 26.250 191.941 Td /F1 9.8 Tf  [(additional datasets or software that should be added to the pages. We will be happy to work with the laboratories providing )] TJ ET
BT 26.250 180.036 Td /F1 9.8 Tf  [(them, and will either store them locally or provide links to their sites.)] TJ ET
BT 26.250 143.433 Td /F4 12.0 Tf  [(Competing Interests)] TJ ET
BT 26.250 123.479 Td /F1 9.8 Tf  [(The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 86.877 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 66.922 Td /F1 9.8 Tf  [(The authors thank the editors and two anonymous reviewers for their very helpful suggestions on the manuscript. )] TJ ET
BT 26.250 55.018 Td /F1 9.8 Tf  [(Correspondence should be sent to CRL. The research was supported by the US National Science Foundation DEB 0733029, )] TJ ET
BT 26.250 43.113 Td /F1 9.8 Tf  [(and by Microsoft Research through support to TW.)] TJ ET
Q
q
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BT 26.250 767.476 Td /F1 9.8 Tf  [(empirical and simulated datasets are provided. Taken as a whole, these datasets have properties that are typical both of )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(markers currently used in large-scale phylogeny estimation and of markers that have evolved under high rates of indels, and are )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(thus extremely difficult to align.)] TJ ET
BT 26.250 724.262 Td /F1 9.8 Tf  [(In addition to the simulated datasets for phylogeny estimation, a simulated amino acid dataset is included )] TJ ET
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BT 482.014 724.262 Td /F1 9.8 Tf  [([14])] TJ ET
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BT 498.277 724.262 Td /F1 9.8 Tf  [(, which has )] TJ ET
BT 26.250 712.357 Td /F1 9.8 Tf  [(sequences that were generated using Rose )] TJ ET
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BT 217.018 712.357 Td /F1 9.8 Tf  [([11])] TJ ET
0.271 0.267 0.267 rg
BT 233.281 712.357 Td /F1 9.8 Tf  [( and ranging from 20 to 100 taxa. Several additional empirical amino acid )] TJ ET
BT 26.250 700.452 Td /F1 9.8 Tf  [(datasets are also included \(BAliBASE )] TJ ET
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BT 191.532 700.452 Td /F1 9.8 Tf  [([15])] TJ ET
0.271 0.267 0.267 rg
BT 207.795 700.452 Td /F1 9.8 Tf  [(, OXBench )] TJ ET
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BT 257.657 700.452 Td /F1 9.8 Tf  [([16])] TJ ET
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BT 273.920 700.452 Td /F1 9.8 Tf  [(, PREFAB )] TJ ET
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BT 321.061 700.452 Td /F1 9.8 Tf  [([17])] TJ ET
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BT 337.324 700.452 Td /F1 9.8 Tf  [(, SABmark )] TJ ET
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BT 386.630 700.452 Td /F1 9.8 Tf  [([18])] TJ ET
0.271 0.267 0.267 rg
BT 402.892 700.452 Td /F1 9.8 Tf  [(\).)] TJ ET
BT 26.250 681.048 Td /F1 9.8 Tf  [(The empirical benchmark datasets for testing multiple sequence alignment include datasets with highly reliable curated )] TJ ET
BT 26.250 669.143 Td /F1 9.8 Tf  [(sequence alignments that have been carefully validated by the community. The gold standard for this sort of dataset is Robin )] TJ ET
BT 26.250 657.238 Td /F1 9.8 Tf  [(Gutell�s Comparative RNA Website \(CRW\) )] TJ ET
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BT 213.148 657.238 Td /F1 9.8 Tf  [([19])] TJ ET
0.271 0.267 0.267 rg
BT 229.411 657.238 Td /F1 9.8 Tf  [(. The curated alignments provided in CRW are based upon secondary structural )] TJ ET
BT 26.250 645.333 Td /F1 9.8 Tf  [(information, which is particularly helpful where the mature rRNA is double stranded due to sequence complementarity.)] TJ ET
BT 26.250 608.731 Td /F4 12.0 Tf  [(Benchmarks for supertree methods)] TJ ET
BT 26.250 588.777 Td /F1 9.8 Tf  [(Finally, we provide benchmarks for testing supertree methods. As with the other benchmark collections, we provide both )] TJ ET
BT 26.250 576.872 Td /F1 9.8 Tf  [(empirical \(Table 3\) and simulated )] TJ ET
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BT 173.085 576.872 Td /F1 9.8 Tf  [([20])] TJ ET
0.271 0.267 0.267 rg
BT 189.348 576.872 Td /F1 9.8 Tf  [( supertree datasets, and include datasets with different properties \(such as the number of )] TJ ET
BT 26.250 564.967 Td /F1 9.8 Tf  [(source trees, and the taxon sampling strategies used to produce the source trees\).)] TJ ET
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26.250 435.411 555.000 119.675 re f
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26.625 553.961 155.724 0.750 re f
182.349 553.961 170.980 0.750 re f
353.329 553.961 91.240 0.750 re f
444.570 553.961 136.305 0.750 re f
26.625 538.205 0.750 16.506 re f
580.125 538.205 0.750 16.506 re f
0.271 0.267 0.267 rg
BT 33.000 544.481 Td /F4 9.8 Tf  [(Table 3)] TJ ET
BT 66.599 544.481 Td /F1 9.8 Tf  [( . Empirical supertree datasets.)] TJ ET
0.000 0.000 0.000 rg
26.625 538.205 155.724 1.000 re f
0.267 0.267 0.267 rg
26.625 522.574 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.000 528.850 Td /F4 9.8 Tf  [(Dataset)] TJ ET
0.000 0.000 0.000 rg
182.349 538.205 170.980 1.000 re f
0.271 0.267 0.267 rg
BT 188.349 528.850 Td /F4 9.8 Tf  [(Taxonomic Range)] TJ ET
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353.329 538.205 91.240 1.000 re f
0.271 0.267 0.267 rg
BT 359.329 528.850 Td /F4 9.8 Tf  [(Total Taxa)] TJ ET
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444.570 538.205 136.305 1.000 re f
0.267 0.267 0.267 rg
580.125 522.574 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.570 528.850 Td /F4 9.8 Tf  [(Number of Source Trees)] TJ ET
0.000 0.000 0.000 rg
26.625 522.574 156.099 1.000 re f
0.267 0.267 0.267 rg
26.625 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 33.375 512.719 Td /F1 9.8 Tf  [(McMahon and Sanderson )] TJ ET
0.267 0.267 0.267 rg
BT 147.723 512.719 Td /F1 9.8 Tf  [([21])] TJ ET
0.000 0.000 0.000 rg
181.974 522.574 171.730 1.000 re f
0.267 0.267 0.267 rg
181.974 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 188.724 512.719 Td /F1 9.8 Tf  [(Comprehensive papilionoid legumes)] TJ ET
0.000 0.000 0.000 rg
352.954 522.574 91.990 1.000 re f
0.267 0.267 0.267 rg
352.954 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 359.704 512.719 Td /F1 9.8 Tf  [(2,228)] TJ ET
0.000 0.000 0.000 rg
444.195 522.574 136.680 1.000 re f
0.267 0.267 0.267 rg
444.195 506.692 0.750 16.881 re f
580.125 506.692 0.750 16.881 re f
0.271 0.267 0.267 rg
BT 450.945 512.719 Td /F1 9.8 Tf  [(39)] TJ ET
0.267 0.267 0.267 rg
26.625 506.692 156.099 0.750 re f
26.625 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 496.837 Td /F1 9.8 Tf  [(Cardillo et al. )] TJ ET
0.267 0.267 0.267 rg
BT 92.977 496.837 Td /F1 9.8 Tf  [([22])] TJ ET
181.974 506.692 171.730 0.750 re f
181.974 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 496.837 Td /F1 9.8 Tf  [(Marsupials)] TJ ET
0.267 0.267 0.267 rg
352.954 506.692 91.990 0.750 re f
352.954 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 496.837 Td /F1 9.8 Tf  [(267)] TJ ET
0.267 0.267 0.267 rg
444.195 506.692 136.680 0.750 re f
444.195 490.811 0.750 16.631 re f
580.125 490.811 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 496.837 Td /F1 9.8 Tf  [(158)] TJ ET
0.267 0.267 0.267 rg
26.625 490.811 156.099 0.750 re f
26.625 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 480.956 Td /F1 9.8 Tf  [(Beck et al. )] TJ ET
0.267 0.267 0.267 rg
BT 81.608 480.956 Td /F1 9.8 Tf  [([23])] TJ ET
181.974 490.811 171.730 0.750 re f
181.974 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 480.956 Td /F1 9.8 Tf  [(Placental mammals)] TJ ET
0.267 0.267 0.267 rg
352.954 490.811 91.990 0.750 re f
352.954 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 480.956 Td /F1 9.8 Tf  [(116)] TJ ET
0.267 0.267 0.267 rg
444.195 490.811 136.680 0.750 re f
444.195 474.930 0.750 16.631 re f
580.125 474.930 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 480.956 Td /F1 9.8 Tf  [(726)] TJ ET
0.267 0.267 0.267 rg
26.625 474.930 156.099 0.750 re f
26.625 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 33.375 465.075 Td /F1 9.8 Tf  [(Kennedy and Page )] TJ ET
0.267 0.267 0.267 rg
BT 119.019 465.075 Td /F1 9.8 Tf  [([24])] TJ ET
181.974 474.930 171.730 0.750 re f
181.974 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 188.724 465.075 Td /F1 9.8 Tf  [(Seabirds)] TJ ET
0.267 0.267 0.267 rg
352.954 474.930 91.990 0.750 re f
352.954 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 359.704 465.075 Td /F1 9.8 Tf  [(121)] TJ ET
0.267 0.267 0.267 rg
444.195 474.930 136.680 0.750 re f
444.195 459.049 0.750 16.631 re f
580.125 459.049 0.750 16.631 re f
0.271 0.267 0.267 rg
BT 450.945 465.075 Td /F1 9.8 Tf  [(7)] TJ ET
0.267 0.267 0.267 rg
26.625 459.049 155.724 0.750 re f
0.000 0.000 0.000 rg
26.625 435.661 155.724 1.000 re f
0.267 0.267 0.267 rg
26.625 435.661 0.750 24.138 re f
0.271 0.267 0.267 rg
BT 33.000 442.069 Td /F1 9.8 Tf  [(Wojciechowski et al. )] TJ ET
0.267 0.267 0.267 rg
BT 123.480 442.069 Td /F1 9.8 Tf  [([25])] TJ ET
182.349 459.049 170.980 0.750 re f
0.000 0.000 0.000 rg
182.349 435.661 170.980 1.000 re f
0.271 0.267 0.267 rg
BT 188.349 449.569 Td /F1 9.8 Tf  [(Temperate herbaceous papilionoid )] TJ ET
BT 188.349 441.937 Td /F1 9.8 Tf  [(legumes)] TJ ET
0.267 0.267 0.267 rg
353.329 459.049 91.240 0.750 re f
0.000 0.000 0.000 rg
353.329 435.661 91.240 1.000 re f
0.271 0.267 0.267 rg
BT 359.329 449.569 Td /F1 9.8 Tf  [(558)] TJ ET
0.267 0.267 0.267 rg
444.570 459.049 136.305 0.750 re f
0.000 0.000 0.000 rg
444.570 435.661 136.305 1.000 re f
0.267 0.267 0.267 rg
580.125 435.661 0.750 24.138 re f
0.271 0.267 0.267 rg
BT 450.570 449.569 Td /F1 9.8 Tf  [(19)] TJ ET
BT 26.250 371.190 Td /F4 12.0 Tf  [(Software for generating datasets)] TJ ET
BT 26.250 351.235 Td /F1 9.8 Tf  [(The collection of simulation software is useful for three aspects of producing simulated datasets: generating simulated )] TJ ET
BT 26.250 339.331 Td /F1 9.8 Tf  [(phylogenetic trees \(e.g., r8s )] TJ ET
0.267 0.267 0.267 rg
BT 149.266 339.331 Td /F1 9.8 Tf  [([26])] TJ ET
0.271 0.267 0.267 rg
BT 165.529 339.331 Td /F1 9.8 Tf  [( and Mesquite )] TJ ET
0.267 0.267 0.267 rg
BT 229.479 339.331 Td /F1 9.8 Tf  [([27])] TJ ET
0.271 0.267 0.267 rg
BT 245.742 339.331 Td /F1 9.8 Tf  [(\); evolving sequences on phylogenetic trees \(particularly tools that evolve )] TJ ET
BT 26.250 327.426 Td /F1 9.8 Tf  [(sequences with both substitution and indel events\) and tools for post-processing model trees in order to deviate from the model )] TJ ET
BT 26.250 315.521 Td /F1 9.8 Tf  [(assumptions \(such as the molecular clock\).)] TJ ET
BT 26.250 278.919 Td /F4 12.0 Tf  [(Conclusions)] TJ ET
BT 26.250 258.964 Td /F1 9.8 Tf  [(We hope that having these benchmark datasets in a single location will facilitate research on large-scale phylogenetic methods )] TJ ET
BT 26.250 247.060 Td /F1 9.8 Tf  [(and enhance the reproducibility of work based upon the datasets. We also hope that posting simulation tools that are capable of )] TJ ET
BT 26.250 235.155 Td /F1 9.8 Tf  [(generating large-scale phylogenetic datasets will promote the generation of new benchmark datasets for use by the community.)] TJ ET
BT 26.250 215.750 Td /F1 9.8 Tf  [(We conceive of these pages as an evolving resource for the community and welcome input that would improve or expand them. )] TJ ET
BT 26.250 203.845 Td /F1 9.8 Tf  [(We invite readers to contact us if they wish to contribute benchmark datasets or software to this resource or if they know of )] TJ ET
BT 26.250 191.941 Td /F1 9.8 Tf  [(additional datasets or software that should be added to the pages. We will be happy to work with the laboratories providing )] TJ ET
BT 26.250 180.036 Td /F1 9.8 Tf  [(them, and will either store them locally or provide links to their sites.)] TJ ET
BT 26.250 143.433 Td /F4 12.0 Tf  [(Competing Interests)] TJ ET
BT 26.250 123.479 Td /F1 9.8 Tf  [(The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 86.877 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 66.922 Td /F1 9.8 Tf  [(The authors thank the editors and two anonymous reviewers for their very helpful suggestions on the manuscript. )] TJ ET
BT 26.250 55.018 Td /F1 9.8 Tf  [(Correspondence should be sent to CRL. The research was supported by the US National Science Foundation DEB 0733029, )] TJ ET
BT 26.250 43.113 Td /F1 9.8 Tf  [(and by Microsoft Research through support to TW.)] TJ ET
Q
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BT 25.000 19.825 Td /F1 11.0 Tf  [(PLOS Currents Tree of Life)] TJ ET

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BT 26.250 683.883 Td /F1 9.8 Tf  [(models. Bioinformatics 22\(21\):2688-2690.)] TJ ET
BT 26.250 664.479 Td /F1 9.8 Tf  [(3.)] TJ ET
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BT 26.250 652.574 Td /F1 9.8 Tf  [(the maximum likelihood criterion. In Section of Integrative Biology, School of Biological Sciences, University of Texas at Austin: )] TJ ET
BT 26.250 640.669 Td /F1 9.8 Tf  [(Austin.)] TJ ET
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BT 38.132 621.264 Td /F1 9.8 Tf  [(Var�n, A., L.S. Vinh, and W.C. Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics, )] TJ ET
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BT 26.250 527.336 Td /F1 9.8 Tf  [(7.)] TJ ET
BT 38.132 527.336 Td /F1 9.8 Tf  [(Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. )] TJ ET
BT 26.250 515.431 Td /F1 9.8 Tf  [(M�ller, N. Pande, Z. Shang, N. Yu, R. R. Gutell. 2002. The Comparative RNA Web \(CRW\) Site: An Online Database of )] TJ ET
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BT 26.250 421.503 Td /F1 9.8 Tf  [(10.)] TJ ET
BT 43.553 421.503 Td /F1 9.8 Tf  [(Price, M. N., P. S. Dehal, A. P. Arkin. 2010. FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. )] TJ ET
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BT 26.250 358.884 Td /F1 9.8 Tf  [(along phylogenetic trees. Comput Appl Biosci 13:235.)] TJ ET
BT 26.250 339.479 Td /F1 9.8 Tf  [(13.)] TJ ET
BT 43.553 339.479 Td /F1 9.8 Tf  [(Guo, S., Wang,L.-S., Kim, J. 2009. Large-scale simulation of RNA macroevolution by an energy-dependent fitness model. )] TJ ET
BT 26.250 327.574 Td /F1 9.8 Tf  [(arXiv:0912.2326v1 [q-bio.PE].)] TJ ET
BT 26.250 308.169 Td /F1 9.8 Tf  [(14.)] TJ ET
BT 43.553 308.169 Td /F1 9.8 Tf  [(Wang, L-S., J. Leebens-Mack, P. K. Wall, K. Beckmann, C. W. dePamphilis, T. Warnow. 2009. The Impact of Multiple )] TJ ET
BT 26.250 296.265 Td /F1 9.8 Tf  [(Protein Sequence Alignment on Phylogenetic Estimation. EEE/ACM Transactions on Computational Biology and Bioinformatics )] TJ ET
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BT 43.553 264.955 Td /F1 9.8 Tf  [(Thompson, J. D., P. Koehl, R. Ripp, O. Poch. 2005. BAliBASE 3.0: Latest developments of the multiple sequence alignment )] TJ ET
BT 26.250 253.050 Td /F1 9.8 Tf  [(benchmark. Proteins 61:127-136.)] TJ ET
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BT 43.553 171.027 Td /F1 9.8 Tf  [(Van Walle. Available from: http://bioinformatics.vub.ac.be/databases/databases.html)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 162.541 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
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BT 43.553 143.991 Td /F1 9.8 Tf  [(Gutell, R. Available from: http://www.rna.ccbb.utexas.edu/CAR/)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 135.505 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
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BT 43.553 116.955 Td /F1 9.8 Tf  [(Swenson, M. S., F. Barban�on, C. Linder, and T. Warnow. 2010. A simulation study comparing supertree and combined )] TJ ET
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BT 43.553 85.645 Td /F1 9.8 Tf  [(McMahon, M. and M. Sanderson. 2006. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid )] TJ ET
BT 26.250 73.740 Td /F1 9.8 Tf  [(legumes. Systematic Biology 55:818-836.)] TJ ET
BT 26.250 54.336 Td /F1 9.8 Tf  [(22.)] TJ ET
BT 43.553 54.336 Td /F1 9.8 Tf  [(Cardillo, M., O. R. P. Bininda-Emonds, E. Boakes, and A. Purvis. 2004. A species-level phylogenetic supertree of )] TJ ET
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BT 26.250 664.479 Td /F1 9.8 Tf  [(3.)] TJ ET
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BT 26.250 652.574 Td /F1 9.8 Tf  [(the maximum likelihood criterion. In Section of Integrative Biology, School of Biological Sciences, University of Texas at Austin: )] TJ ET
BT 26.250 640.669 Td /F1 9.8 Tf  [(Austin.)] TJ ET
BT 26.250 621.264 Td /F1 9.8 Tf  [(4.)] TJ ET
BT 38.132 621.264 Td /F1 9.8 Tf  [(Var�n, A., L.S. Vinh, and W.C. Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics, )] TJ ET
BT 26.250 609.360 Td /F1 9.8 Tf  [(2010. 26: in press.)] TJ ET
BT 26.250 589.955 Td /F1 9.8 Tf  [(5.)] TJ ET
BT 38.132 589.955 Td /F1 9.8 Tf  [(Liu, K., et al. 2009. Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees. Science )] TJ ET
BT 26.250 578.050 Td /F1 9.8 Tf  [(324\(5934\):1561-1564.)] TJ ET
BT 26.250 558.645 Td /F1 9.8 Tf  [(6.)] TJ ET
BT 38.132 558.645 Td /F1 9.8 Tf  [(Ronquist, F. and J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics )] TJ ET
BT 26.250 546.741 Td /F1 9.8 Tf  [(19\(12\):1572-1574.)] TJ ET
BT 26.250 527.336 Td /F1 9.8 Tf  [(7.)] TJ ET
BT 38.132 527.336 Td /F1 9.8 Tf  [(Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. )] TJ ET
BT 26.250 515.431 Td /F1 9.8 Tf  [(M�ller, N. Pande, Z. Shang, N. Yu, R. R. Gutell. 2002. The Comparative RNA Web \(CRW\) Site: An Online Database of )] TJ ET
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BT 38.132 484.122 Td /F1 9.8 Tf  [(Elgavish T., J. J. Cannone, J. C. Lee, S. C. Harvey, R. R. Gutell. 2001. AA.AG@Helix.Ends: A:A and A:G Base-pairs at the )] TJ ET
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BT 43.553 421.503 Td /F1 9.8 Tf  [(Price, M. N., P. S. Dehal, A. P. Arkin. 2010. FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. )] TJ ET
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BT 43.553 390.193 Td /F1 9.8 Tf  [(Stoye, J., D. Evers, F. Meyer. 1998. Rose: generating sequence families. Bioinformatics 14:157-163.)] TJ ET
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BT 43.553 370.788 Td /F1 9.8 Tf  [(Rambaut, A. and N.C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution )] TJ ET
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BT 43.553 339.479 Td /F1 9.8 Tf  [(Guo, S., Wang,L.-S., Kim, J. 2009. Large-scale simulation of RNA macroevolution by an energy-dependent fitness model. )] TJ ET
BT 26.250 327.574 Td /F1 9.8 Tf  [(arXiv:0912.2326v1 [q-bio.PE].)] TJ ET
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BT 43.553 308.169 Td /F1 9.8 Tf  [(Wang, L-S., J. Leebens-Mack, P. K. Wall, K. Beckmann, C. W. dePamphilis, T. Warnow. 2009. The Impact of Multiple )] TJ ET
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BT 43.553 264.955 Td /F1 9.8 Tf  [(Thompson, J. D., P. Koehl, R. Ripp, O. Poch. 2005. BAliBASE 3.0: Latest developments of the multiple sequence alignment )] TJ ET
BT 26.250 253.050 Td /F1 9.8 Tf  [(benchmark. Proteins 61:127-136.)] TJ ET
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BT 43.553 233.646 Td /F1 9.8 Tf  [(Raghava, G. P. S., S. M. J. Searle, P. C. Audley, J. D. Barber, G. J. Barton. 2003. OXBench: A benchmark for evaluation of )] TJ ET
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BT 26.250 135.505 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
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BT 43.553 54.336 Td /F1 9.8 Tf  [(Cardillo, M., O. R. P. Bininda-Emonds, E. Boakes, and A. Purvis. 2004. A species-level phylogenetic supertree of )] TJ ET
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