PhyloBayes statistics

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Number of citations per year for the bioinformatics software tool PhyloBayes

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PhyloBayes specifications


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


No version available

Publication for PhyloBayes

PhyloBayes citations


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

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

[…] ogram IQ-TREE version 1.5.1. Branch support for each internode was evaluated with 100 rapid bootstrapping replicates using RAxML. Because running an analysis using the site-heterogeneous CAT model in PhyloBayes is computationally intractable for our concatenated dataset, the C60 model (a maximum likelihood variant of Bayesian CAT model) implemented in IQ-TREE was used to infer ML phylogeny with pa […]


GATC: a genetic algorithm for gene tree construction under the Duplication Transfer Loss model of evolution

BMC Genomics
PMCID: 5954287
PMID: 29764363
DOI: 10.1186/s12864-018-4455-x

[…] , the gene families were retrieved from HOGENOM [] and multiple alignments were performed on these families with Muscle []. For each alignment, an MCMC sample of at least 3000 trees was obtained with PhyloBayes [] and used to reconstruct an amalgamated tree with ALE []. These trees were used to simulate new multiple alignments of artifical sequences under the LG model with a gamma distribution. We […]


Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)

Sci Rep
PMCID: 5935716
PMID: 29728615
DOI: 10.1038/s41598-018-25338-3

[…] s, with tree sampling every 1000 generations and a burn-in of 25%. In IQ-TREE analyses, the number of bootstrap replicates was set to 1000 with CAT model (C20 + 4 G). The CAT-GTR model was applied in PhyloBayes analyses with independent Markov chain runs of 8000 and a burn-in of 1000 and subsample of 10 trees. Pelecinus polyturator (Proctotrupoidea: Pelecinidae) and Vanhornia eucnemidarumI (Procto […]


Genes for de novo biosynthesis of omega 3 polyunsaturated fatty acids are widespread in animals

Sci Adv
PMCID: 5931762
PMID: 29732410
DOI: 10.1126/sciadv.aar6849

[…] Information Criterion. The ML phylogenetic inference was performed using RAxML with 100 rapid bootstrap replicates and 20 ML searches. The Bayesian inference was applied using MrBayes v.3.2.1 () and PhyloBayes MPI v.1.7a (). MrBayes was run with four Markov chains incrementally heated with the default values. Each chain started with a randomly generated tree and ran for 1x107 generations with sam […]


Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

Front Zool
PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] tion was used with 1000 bootstrap iterations []. The iQ analyses were run with the -spp parameter allowing each partition to have its own evolutionary rate. Bayesian inference (BI) was conducted with PhyloBayes [] on the CIPRES web portal [] using two independent chains under a GTRCAT model. Analyses were run checking for convergence every 1800 s excluding the first 500 cycles, and the runs were s […]


Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

BMC Evol Biol
PMCID: 5924465
PMID: 29703131
DOI: 10.1186/s12862-018-1186-1

[…] confidence score (i.e., below 0.93), as well as positions present in less than 25% of the species. The sequence alignments are provided in Additional file .Phylogenetic inference was conducted using PhyloBayes v3.3b. We used the CAT + GTR + Γ mixture model for the Bayesian analysis. Bayesian analyses were conducted with three chains run for 90,000 cycles each and sampled every 10 cycles, with the […]

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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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