PQ, a new program for phylogeny reconstruction

Penzar, Dmitry; Krivozubov, Mikhail; Spirin, Sergei A.

doi:10.1186/s12859-018-2399-4

Cited by 4 publications

(10 citation statements)

References 24 publications

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“…Thus, on the 45-sequence combined set, FastME using SPR search, the BME criterion, and p-distance produced a tree closer to the reference than the RAxML tree in 989 cases and, in 657 cases, outputted a more distant tree, with Z = −5.87. The superiority of distance methods over ML on natural sequences has long been shown [3,4,5]. In particular, Gonnet's article [4] was based on a substantial amount of data, published in the popular open access journal 'BMC Bioinformatics', and presumably should close the problem.…”

Section: Comparison Of Six Methods With Optimised Parametersmentioning

confidence: 99%

“…In this study, we used the following phylogenetic programs: TNT [9], RAxML [10], MrBayes [11], PQ [5], TREE-PUZZLE [12], and FastME [13]. A description of the versions and options that were used can be found in the Supplementary text.…”

Section: Phylogenetic Programsmentioning

confidence: 99%

“…4 Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia. 5 Gamaleya Center of Epidemiology and Microbiology, Moscow, Russia. 6 Institute of Agricultural Biotechnology, Moscow, Russia.…”

Section: Abbreviationsmentioning

confidence: 99%

“…An evaluation of the relative accuracy of programs, or the choice of options, is often based on simulated sequence alignments [1,2]. However, comparisons of phylogenetic programs performed on alignments of natural sequences [3,4,5] give significantly different results from those made on simulations. This suggests that comparisons made with simulated alignments may not be sufficiently accurate.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

PhyloBench: a Benchmark for Evaluating Phylogenetic Programs

Spirin

Sigorskikh

Efremov

et al. 2023

Preprint

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Motivation. Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options.Choosing a program, options, and parameters can be a nontrivial task.No benchmark for comparison of phylogenetic programs on real protein sequences is publicly available. Results. We have developed PhyloBench, a benchmark for evaluating the quality of phylogenetic inference, and used it to test a number of popular phylogenetic programs. PhyloBench is based on natural, not simulated, protein sequences of orthologous evolutionary domains. The measure of accuracy of an inferred tree is its distance to the corresponding species tree. A number of tree-to-tree distance measures were tested. The most reliable results were obtained using the Robinson–Foulds distance. Our results confirmed recent findings that distance methods are more accurate than maximum likelihood and maximum parsimony. We tested the bayesian program MrBayes on natural protein sequences and found that it is superior to maximum likelihood, but inferior to distance methods. Of the methods we tested, the Balanced Minimum Evolution method implemented in FastME yielded the best results. Availability. Benchmark alignments and reference trees are available at https://mouse.belozersky.msu.ru/tools/phylobench/ together with a web-interface that allows for a semi-automatic comparison of a user's method with a number of popular programs.

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Section: Comparison Of Six Methods With Optimised Parametersmentioning

confidence: 99%

Section: Phylogenetic Programsmentioning

confidence: 99%

Section: Abbreviationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

PhyloBench: a Benchmark for Evaluating Phylogenetic Programs

Spirin

Sigorskikh

Efremov

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…There are few studies where comparisons of phylogenetic programs were performed on alignments of real sequences of orthologous proteins and the accuracy was evaluated according to proximity to a species tree [4,5,6]. These studies provided significantly different results from those made on simulations.…”

Section: Introductionmentioning

confidence: 99%

PhyloBench: a Benchmark for Evaluating Phylogenetic Programs

Spirin,

Sigorskikh,

Efremov

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Motivation. Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options. Choosing a program, options, and parameters can be a nontrivial task. No benchmark for comparison of phylogenetic programs on real protein sequences is publicly available. Results. We have developed PhyloBench, a benchmark for evaluating the quality of phylogenetic inference, and used it to test a number of popular phylogenetic programs. PhyloBench is based on natural, not simulated, protein sequences of orthologous evolutionary domains. The measure of accuracy of an inferred tree is its distance to the corresponding species tree. A number of tree-to-tree distance measures were tested. The most reliable results were obtained using the Robinson–Foulds distance. Our results confirmed recent findings that distance methods are more accurate than maximum likelihood and maximum parsimony. We tested the bayesian program MrBayes on natural protein sequences and found that it is superior to maximum likelihood, but inferior to distance methods. Of the methods we tested, the Balanced Minimum Evolution method implemented in FastME yielded the best results. Availability. Alignments and reference species trees are available at https://mouse.belozersky.msu.ru/tools/phylobench/ together with a web-interface that allows for a semi-automatic comparison of a user’s method with a number of popular programs.

show abstract

PhyloBench: A Benchmark for Evaluating Phylogenetic Programs

Spirin,

Sigorskikh,

Efremov

et al. 2024

Molecular Biology and Evolution

View full text Add to dashboard Cite

Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options. Choosing a program, options, and parameters can be a nontrivial task. No benchmark for comparison of phylogenetic programs on real protein sequences was publicly available. We have developed PhyloBench, a benchmark for evaluating the quality of phylogenetic inference, and used it to test a number of popular phylogenetic programs. PhyloBench is based on natural, not simulated, protein sequences of orthologous evolutionary domains. The measure of accuracy of an inferred tree is its distance to the corresponding species tree. A number of tree-to-tree distance measures were tested. The most reliable results were obtained using the Robinson–Foulds distance. Our results confirmed recent findings that distance methods are more accurate than maximum likelihood (ML) and maximum parsimony. We tested the bayesian program MrBayes on natural protein sequences and found that, on our datasets, it performs better than ML, but worse than distance methods. Of the methods we tested, the Balanced Minimum Evolution method implemented in FastME yielded the best results on our material. Alignments and reference species trees are available at https://mouse.belozersky.msu.ru/tools/phylobench/ together with a web-interface that allows for a semi-automatic comparison of a user’s method with a number of popular programs.

show abstract

PQ, a new program for phylogeny reconstruction

Cited by 4 publications

References 24 publications

PhyloBench: a Benchmark for Evaluating Phylogenetic Programs

PhyloBench: a Benchmark for Evaluating Phylogenetic Programs

PhyloBench: a Benchmark for Evaluating Phylogenetic Programs

PhyloBench: A Benchmark for Evaluating Phylogenetic Programs

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