BayesTraits protocols

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BayesTraits specifications

Information


Unique identifier OMICS_09938
Name BayesTraits
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andrew Meade <>

Publication for BayesTraits

BayesTraits in pipelines

 (11)
2017
PMCID: 5310583
PMID: 28077686
DOI: 10.1098/rsbl.2016.0783

[…] using functions from the package phytools [] in r []. correlated evolution between cavity nesting and iris colour and parental care and iris colour were analysed using the discrete module [] in bayestraits []. this tests whether the evolutionary model in which two traits evolved dependently on one another is significantly better than the evolutionary model in which two traits evolved […]

2017
PMCID: 5543309
PMID: 28763051
DOI: 10.1038/ncomms16047

[…] complementary approaches: mp using the ancestral.pars function of the phangorn 2.0.2 package in r, ml using the raydisc function of the corhmm 1.18 package in r, and a bayesian rjmcmc approach using bayestraits 2 (ref. ). mp and ml reconstructions were conducted on the mcc tree from each beast analysis, whereas bayesian rjmcmc analyses were conducted on collections of at least 1,000 trees […]

2016
PMCID: 5055826
PMID: 27498812
DOI: 10.1093/aob/mcw151

[…] a posterior sample of trees, which we rooted on cornales. fig. 2. fig. 3. , we used our posterior sample of trees to run comparative analyses of transitions between scalariform and simple using bayestraits v. 2.0 (), which we ran as markov chain monte carlo (mcmc) analyses using an exponential prior for the transition rates and using a stepping stone sampler () to obtain estimates […]

2016
PMCID: 5147985
PMID: 27936063
DOI: 10.1371/journal.pone.0167773

[…] a phylogenetic tree. in order not to confuse the lineages within basidiomycetes by rooting the tree in one of them, the outgroup class ii hydrophobin of paracoccoides brasiliensis was chosen., bayestraits version 2.0 [] was used to obtain ancestral states by maximum likelihood (default) and bayesian method (default, burnin 50000). the calculation of abundance of tricholoma under a specific […]

2014
PMCID: 4226868
PMID: 25346285
DOI: 10.1186/1471-2164-15-939

[…] maximum clade credibility tree was constructed in treeannotator v 1.6.2 in the beast package []. regressions of the phylogeny and the microsatellite relative abundance and length were performed with bayestraits [] using model a and b, and followed by a log likelihood test, to test for a relationship between phylogeny and microsatellite traits. species were grouped based on microsatellite […]


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BayesTraits in publications

 (170)
PMCID: 5951845
PMID: 29760391
DOI: 10.1038/s41467-018-04265-x

[…] and pensile attachment) was used by <10% of all families and almost all of which were passerines (figs.  and )., to examine the evolutionary trajectories of the three nest characters, we used bayestraits– to reconstruct ancestral character states for each character across the avian family phylogeny. to account for phylogenetic uncertainty, the ancestral state reconstruction was based […]

PMCID: 5889631
PMID: 29555760
DOI: 10.1073/pnas.1714558115

[…] of analyses were identical., correlated evolution was investigated using a bayesian reversible-jump markov chain monte carlo approach implemented in the “discrete” component of the computer package bayestraits (). this method involves the testing of an independent model (in which rates are independent) against a dependent model (in which rates can covary). each set of analyses involved four […]

PMCID: 5842878
PMID: 29466405
DOI: 10.1371/journal.pone.0191529

[…] obtained from the examination of herbarium specimens, the taxonomic literature, and online databases cited above. transition rate estimation and ancestral character reconstruction were performed in bayestraits 2.0.2 []. analyses were conducted employing a continuous-time markov model of trait evolution with two instantaneous rates representing all possible state changes (qannual→perennial […]

PMCID: 5817949
PMID: 29432584
DOI: 10.1093/gbe/evy030

[…] can be generated. following whole-genome sequencing, a core-genome phylogeny was constructed under a general-time reversible model, and was used to infer phylogenetic-controlled correlations using bayestraits (; see materials and methods for more details). we find strong evidence for trade-offs associated with antibiotic resistance (). resistances to both ceftazidime and ciprofloxacin […]

PMCID: 5798147
PMID: 29360978
DOI: 10.1093/gbe/evy013

[…] (). to test this prediction, we first searched for evidence of punctuated molecular evolution across the best ml phylogeny using a phylogenetic generalized least squares (pgls) regression in bayestraits v3.0 (), which incorporates a species phylogeny and weights data points according to shared ancestry. we removed the nonamniote outgroup and applied a continuous model to the phylogenetic […]


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BayesTraits institution(s)
School of Animal and Microbial Sciences, University of Reading, Whiteknights Reading, UK

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