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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 citations

 (433)
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

[…] 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 […]

library_books

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

2018
BMC Genomics
PMCID: 5954287
PMID: 29764363
DOI: 10.1186/s12864-018-4455-x

[…] n the reconstruction of gene trees.Standard phylogenetic tools are based on maximum likelihood (ML) or bayesian methods reconstructing a tree from gene sequences (e.g. PhyML [], RAxML [], MrBayes [], PhyloBayes []). However, for a variety of reasons due, not only to technical limitations but also to the data itself (sequences too close to each other or conversely too divergent), sequence-only meth […]

library_books

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

2018
Sci Rep
PMCID: 5935716
PMID: 29728615
DOI: 10.1038/s41598-018-25338-3

[…] of the 13 protein-coding genes. Nucleotide sequences were aligned by codon using MAFFT version 7.205. Phylogenetic relationships were reconstructed with MrBayes version 3.2.5, IQ-TREE web server and PhyloBayes-MPI. In MrBayes analyses, matrices were partitioned by codon position. Then, we used PartitionFinder version 1.1.1 to determine the best partition and substitution models. Four independent […]

library_books

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

2018
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 […]

library_books

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

2018
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 […]

library_books

Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

2018
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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