PhyloBayes protocols

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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Publication for PhyloBayes

PhyloBayes IN pipelines

 (9)
2017
PMCID: 5615479
PMID: 28950916
DOI: 10.1186/s13071-017-2381-4

[…] randomly) and 540 protein sequences were retained by the cd-hit tool [23]. the sequences were aligned using the mafft algorithm with default parameters [24]. the bayesian analysis was performed in phylobayes 4.1 with two monte carlo markov chains (mcmc) using the lg model with catfix c20 and poisson [25–28]. the chains were stopped until convergence (maxdif <0.3) for each chain. the mcmc […]

2016
PMCID: 4732765
PMID: 26824644
DOI: 10.1371/journal.pgen.1005836

[…] was deduced by means of mafft [32]. positions containing more than 50% gaps were removed by using gblocks [33]. the resulting msa contained 430 meaningful positions. the program pb (version 3.3 of phylobayes, [15]) with options–cat–gtr was used to compute in four independent monte carlo markov chains (mcmc) 50 000 samples each. the options–cat–gtr induce an infinite mixture model, whose […]

2015
PMCID: 4571573
PMID: 26323765
DOI: 10.1098/rstb.2014.0335

[…] for a conserved position’ b1 = 50, ‘minimum number of sequences for a flank position’ b2 = 50 and ‘allowed gap positions' b5 = a (all). to estimate computing time per family, we measured the time phylobayes took [21] to compute 10 trees based on each alignment. we discarded the decile of the slowest families. for each remaining alignment, we ran two chains using phylobayes, calculating 5500 […]

2015
PMCID: 4571573
PMID: 26323765
DOI: 10.1098/rstb.2014.0335

[…] family, we measured the time phylobayes took [21] to compute 10 trees based on each alignment. we discarded the decile of the slowest families. for each remaining alignment, we ran two chains using phylobayes, calculating 5500 gene trees (discarding the first 500 as burn-in), using the lg model of evolution [44]. in the end, we were able to compute at least one chain for 9596 gene families. […]

2015
PMCID: 5635595
PMID: 26537223
DOI: 10.1093/gbe/evv204

[…] 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, […]

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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