PhyML protocols

PhyML specifications

Information


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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Documentation


Maintainers


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

Information


Unique identifier OMICS_04241
Name PhyML
Interface Web user interface
Restrictions to use None
Input data A single text file containing one or more alignments of DNA or protein sequences.
Input format PHYLIP
Output data NEWICK
Output format A summary of options selected by the user, maximum likelihood estimates of the parameters of the substitution model that were adjusted, the log likelihood of the model given the data and the maximum likelihood phylogeny(ies).
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


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

Publications for PhyML

PhyML IN pipelines

 (403)
2018
PMCID: 5750389
PMID: 29299531
DOI: 10.1128/mSphereDirect.00463-17

[…] species, s protein sequence alignments enabled us to determine the demarcation between s1 and s2 domains based on the position of the s1/s2 cleavage site found in some alphacoronaviruses. phyml was used to generate maximum-likelihood (ml) trees based on whole-genome nucleotide, orf1ab protein, and s protein complete and partial (s1 and s2 domain) alignments. whole-genome, orf1ab […]

2018
PMCID: 5771137
PMID: 29338683
DOI: 10.1186/s12864-017-4429-4

[…] penalty of 1.53; and an offset value of 0.123. a consensus sequence was then created for each species using the default geneious settings. finally, a phylogenetic tree was constructed using the phyml plug-in [51]. the tree was based on an hky85 substitution model [52] and features 100-bootstrap branch support; optimized topology, branch lengths, rates, and nearest-neighbor interchange […]

2018
PMCID: 5773217
PMID: 29346417
DOI: 10.1371/journal.ppat.1006765

[…] the online phylogeny.fr program (http://www.phylogeny.fr/.version2_cgi/index.cgi) with default settings [41,42] was used for multiple sequence alignment (muscle; [43]), phylogenetic analysis (phyml; [44]), and tree rendering (treedyn; [45]) of uxt1 and uxt2 and other nsts. these included transporters of udp-galf (aspergillus fumigatus, af), udp-xyl (homo sapiens, hs, uxt np_116215.1; […]

2018
PMCID: 5775359
PMID: 29352135
DOI: 10.1038/s41598-018-19526-4

[…] resource phylogeny.fr69. the software is based on a built-in pipeline with chaining programs with recognized accuracy as follow: muscle for multiple alignment70, gblocks for alignment refinement71, phyml for tree building72, and treedyn for tree rendering73. all parameters are set up to default, as they are suitable for the investigated virus69., amino acid sequences corresponding to rna […]

2018
PMCID: 5787326
PMID: 29373979
DOI: 10.1186/s12985-018-0931-9

[…] to amplify pepper cryptic virus 2 (pcv-2) rna 2, for phylogenetic analysis, multiple alignments were performed by muscle implemented in seaview v.4.5.4 and the phylogenetic trees were built by phyml software [13–15]. maximum likelihood was used as the criterion to infer phylogenetic relationships between the isolates. the appropriate nucleotide substitution model was selected by jmodeltest […]

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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