PhyML statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PhyML
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Tool usage distribution map

This map represents all the scientific publications referring to PhyML per scientific context
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Associated diseases

This word cloud represents PhyML usage per disease context
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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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Versioning


No version available

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 citations

 (5088)
call_split

Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

2018
Sci Rep
PMCID: 5958079
PMID: 29773850
DOI: 10.1038/s41598-018-26180-3
call_split See protocol

[…] illán-Barcia et al.. MOB families and subfamilies were also defined as in Garcillán-Barcia et al.. MOB relaxase and Rep_3 family phylogenetic analysis was carried out by maximun likelihood (ML) using PhyML 20131016. The best evolutionary model for each multiple alignment was established by ProtTets 2.4. Bootstrap values of 100 were chosen for ML analysis. Rep_3 database sequences used for phylogen […]

library_books

Identification and tissue distribution of chemosensory protein and odorant binding protein genes in Tropidothorax elegans Distant (Hemiptera: Lygaeidae)

2018
Sci Rep
PMCID: 5958050
PMID: 29773848
DOI: 10.1038/s41598-018-26137-6

[…] he matured OBPs and CSPs from T. elegans and other Hemipteran species were performed using MAFFT (http://mafft.cbrc.jp/alignment/server/clustering.html), and phylogenetic trees were constructed using PhyML in Seaview v.4 using the Jones-Taylor-Thomton (JTT) model with 1000-fold bootstrap replication in neighbor-joining method (NJ). […]

library_books

Components of a new gene family of ferroxidases involved in virulence are functionally specialized in fungal dimorphism

2018
Sci Rep
PMCID: 5955967
PMID: 29769603
DOI: 10.1038/s41598-018-26051-x

[…] . Multiple protein sequence alignment was conducted with MUSCLE program, and then curated by Gblocks to select conserved blocks of amino acids. Computational phylogenetic analysis was performed using PhyML software. Phylogenetic relationship was inferred by maximum likelihood-based statistical methods, employing a bootstrapping procedure of 1000 iterations. […]

library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] h MAFFT 7.215 with the “--auto” option and default parameters [], the alignment was optimized with Gblocks 0.91 using options “-b3=10 -b4=3 -b5=n” [] and used for the reconstruction of phylogeny with PhyML 3.1 [] if it was longer than 200 nucleotides and contained on average at least 15 nucleotide differences between the gene pairs. Hasegawa-Kishino-Yano, 85 [] nucleotide substitution model was us […]

library_books

Evolutionary instability of CUG Leu in the genetic code of budding yeasts

2018
Nat Commun
PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] the site-heterogeneous model and to conduct 1000 ultrafast bootstrap replicates (Supplementary Fig. ). Running time was ~25 days with 32 CPUs. Phylogenetic trees for tRNA genes were constructed using PhyML after intron removal and MUSCLE alignment. To calculate the probability of all VLEs appearing outside the Leu0 clade under the hypothesis that they are uniformly distributed across the tree, we […]

library_books

Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing end tracking protein

2018
PLoS Genet
PMCID: 5944918
PMID: 29746462
DOI: 10.1371/journal.pgen.1007221

[…] ignment and gene construction were done using the Geneious R7 software. Multiple alignment was done with the ClustalW algorithm using default settings. A maximum likelihood tree was obtained with the PHYML plugin [], using the Le Gascuel substitution model and bootstrap for branch support (100 bootstraps). A consensus tree was generated where only branches having more than 50% support are shown. H […]


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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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