PhyloBayes specifications

Information


Unique identifier OMICS_02212
Name PhyloBayes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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PhyloBayes article

PhyloBayes citations

 (4)
2017
PMCID: 5469826

[…] the alignment was trimmed at both ends to only include positions covered in all sequences. pairwise sequence similarity was calculated using arb57. phylogenetic trees were calculated using phylobayes71 with the cat model72 and gtr exchange rates. ten independent chains were calculated with 210 generations each. for the final converged tree, all 10 chains were taken into account whereas […]

2016
PMCID: 5164836

[…] for downstream analysis., construction of the multi-protein phylogeny , the 298 single-copy gene alignments were concatenated into a super-protein alignment. a phylogenetic tree was inferred using phylobayes (version 3.3)24 under the cat model25. this is a mixture model that takes into consideration site-specific evolutionary properties (such as rate and profile) within the alignment25. […]

2015
PMCID: 5635595

[…] centre (sonata/2011/03/d/nz2/01435) grants. the authors thank morgan price for access to fasttreemp version with lg matrix support and nicholas lartillot for helpful advice regarding tests of phylobayes-mpi results. they especially acknowledge mukul bansal for advice on maximally parsimonious reconciliation algorithms as well as access to the most current version of dtl-ranger package, […]

2014
PMCID: 4202329

[…] model (lg, gtr, cat-lg, cat-gtr, c20-lg, c20-gtr, c30-lg, c30-gtr, c40-lg, c40-gtr, c50-lg, c50-gtr, c60-lg, c60-gtr, wlsr5-lg, wlsr5-gtr) was performed for comparison using the multicore version of phylobayes mpi v1.4f (lartillot et al. 2009). therefore, the original alignment was split randomly ten times into a learning set (9/10 of the initial data set) and a test set (1/10 of the initial […]

PhyloBayes institution(s)
Laboratoire de Biométrie et Biologie Évolutive, Centre National de la Recherche Scientifique, UMR 5558 Université Lyon 1, Villeurbanne, France; Centre Robert-Cedergren pour la Bioinformatique, Département de Biochimie, Université de Montréal, Québec, Canada

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