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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Open accessAbstract
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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“On the other hand, FastTree was found to be much faster than RAxML and PhyML but reported lower likelihood scores for data sets with both small and large numbers of sequences (Guindon et al. 2010; Price et al. 2010; Liu et al. 2011).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“In these studies, RAxML and PhyML showed largely similar performance in identifying trees of higher likelihood scores (Guindon et al. 2010; Money and Whelan 2012), whereas IQ-TREE exhibited improved efficiency compared with both RAxML and PhyML (Nguyen et al. 2015; Chernomor et al. 2016).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“However, in contrast to previous observations (Guindon et al. 2010), we found that RAxML consistently outperformed PhyML in all data sets.”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“So far, these four programs have only been evaluated using simulated data (Guindon et al. 2010; Price et al. 2010; Liu et al. 2011), and empirical data sets with wide ranges of taxon numbers (e.g., up to 237,882 taxa in Price et al. [2010]) but relatively small numbers of genes (from ∼10 [Price et al. 2010; Liu et al. 2011; Chernomor et al. 2016] to ∼200 [Guindon et al. 2010; Money and Whelan 2012”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“This difference might be due to the small number of alignments examined in the previous study (Guindon et al. 2010) and the numerous updates of both programs since then.”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“Overall, our results at the level of single-gene tree inference are consistent with previous, smaller-scale studies on the better efficiency of IQ-TREE relative to RAxML and PhyML (all using one search per alignment) (Nguyen et al. 2015), and the inferior performance of FastTree in likelihood score maximization when compared with other programs (Guindon et al. 2010; Liu et al. 2011).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“Such differential behavior may be attributed to the distinct algorithmic designs and/or software implementations of the programs on protein and DNA data (Guindon et al. 2010).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“in agreement with previous studies (Guindon et al. 2010; Nguyen et al. 2015), we found that some programs displayed different time efficiency on protein and DNA data sets”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
In the citing paper
“A potential explanation could be that IQ-TREE uses NNI as its topological rearrangement mechanism (Nguyen et al. 2015), whereas RAxML and PhyML are both based on SPR (Stamatakis 2006; Guindon et al. 2010).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Guindon et al. 2010
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Metadata
- Authors
- Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- SIB Swiss Institute of Bioinformatics (CH)
- Corresponding author
- Gascuel, Olivier
- ORCID
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-03-29
- Volume
- 59
- Issue
- 3
- Pages
- 307-321
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2111211467
- Cited by
- 18,376
- References
- 41
- Citations by year
- 2026: 1054 · 2025: 1310 · 2024: 1284 · 2023: 1304 · 2022: 1541 · 2021: 1787 · 2020: 1614 · 2019: 1428 · 2018: 1301 · 2017: 1148 · 2016: 1113 · 2015: 1006 · 2014: 1002 · 2013: 748 · 2012: 507
- FWCI
- 190.74
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Systematic Biology (publishedVersion)
- PubMed (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, other-oa)
- HAL (submittedVersion, other-oa)
- reroDoc Digital Library (submittedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, other-oa)
- ResearchSpace (University of Auckland) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, other-oa)
- ETH Zürich Research Collection
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Agence Nationale de la Recherche
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- PhyML, maximum likelihood phylogenetic inference, nonparametric bootstrap
- MeSH terms
- Algorithms, Classification, Phylogeny, Software, Likelihood Functions
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