PhyML specifications


Unique identifier OMICS_04241
Name PhyML
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes



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  • person_outline Stéphane Guindon <>
  • person_outline Olivier Gascuel <>

PhyML article

PhyML citations

PMCID: 5943581

[…] 4.0 ( and alignments were generated using mafft v7 ( maximum likelihood phylogenetic tree was generated using phyml43 and employing the wag substitution model44 with 100 bootstraps to evaluate branch support. the resulting phylogenetic tree visualizations and annotations were performed using figtree v1.4.2. […]

PMCID: 5905479

[…] pol subtype was determined by rega hiv subtyping tool and maximum likelihood phylogenetics. the presence of pre-treatment drug resistance transmission clades was verified by maximum likelihood tree (phyml 3.0) for subtypes b, c, and f, separately, in both national and regional levels. phylogenetic trees were edited using figtree v1.4.3. we analyzed 1,566 hiv pol sequences from antiretroviral […]

PMCID: 5923463

[…] study and, those of ccdav and cacdav using muscle [27]. a maximum likelihood tree with the rtrev+g amino acid substitution model, inferred as best fit models using prottest [28], was inferred using phyml 3.0 [30] and the tree was midpoint rooted. braches with <0.8 alrt support were collapsed using treegraph2 [26]., all pairwise identities (genome-wide, cp, mp and rep) were determined using […]

PMCID: 5875859

[…] among site rate heterogeneity, a proportion of invariable sites (gtr+i+γ5) [17], and 1,000 bootstrap replicates (using the phyml programme, available at the tree was rooted using a midpoint rooting with figtree software version 1.4.2., genetic distances were determined to analyse genetic variability, and these analyses were conducted using […]

PMCID: 5941160

[…] analysis (234 out of 605). each such msa was given as input to phyml v3.1 (guindon et al . 2010 broken ref.) to reconstruct the maximum likelihood tree. the model of nucleotide substitution for the phyml reconstruction was hky (hasegawa et al. 1985). rate variation among sites was modeled by a discrete gamma distribution with four rate categories (yang 1994)., we generated rooted versions […]

PhyML institution(s)
Methodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS, Universite de Montpellier, Montpellier, France; Department of Statistics, University of Auckland, Auckland, New Zealand; Institute of Computational Science, ETH, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Statistics, University of Oxford, Oxford, UK
PhyML funding source(s)
Supported by ANR projects PlasmoExplore (MD&CA-2006) and MitoSys (BioSYS-2006).

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