BayesTraits pipeline

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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Documentation


Maintainer


  • person_outline Andrew Meade <>

Publication for BayesTraits

BayesTraits IN pipelines

 (18)
2017
PMCID: 5310583
PMID: 28077686
DOI: 10.1098/rsbl.2016.0783

[…] functions from the package phytools [15] in r [16]. correlated evolution between cavity nesting and iris colour and parental care and iris colour were analysed using the discrete module [17] in bayestraits [18]. 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

[…] approaches52: mp using the ancestral.pars function of the phangorn 2.0.2 package53 in r54, ml using the raydisc function of the corhmm 1.18 package55 in r54, and a bayesian rjmcmc approach5657 using bayestraits 2 (ref. 58). 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 […]

2015
PMCID: 4588643
PMID: 26442762
DOI: 10.1002/ece3.1580

[…] states using maximum likelihood and optimized on the moth bayesian topology., we tested the correlation between the occurrence/absence of green‐islands and the occurrence/absence of wolbachia using bayestraits (available on http://www.evolution.rdg.ac.uk) (pagel 1994). we used all 5982 sampled trees of leaf miners identified during the mr bayes search. as polytomies are not allowed […]

2015
PMCID: 4588643
PMID: 26442762
DOI: 10.1002/ece3.1580

[…] using bayestraits (available on http://www.evolution.rdg.ac.uk) (pagel 1994). we used all 5982 sampled trees of leaf miners identified during the mr bayes search. as polytomies are not allowed by bayestraits, they were removed using the multi2di function in the ape package version 3.0–7, which replaces the polytomies by several dichotomies with a zero branch length., for the correlation […]

2014
PMCID: 4161906
PMID: 25159814
DOI: 10.1186/1471-2164-15-721

[…] (“0”). we then estimated the transition rates leading from one state to any other for all e. coli overlapping gene pairs using the bayestrait software package (http://www.evolution.reading.ac.uk/bayestraits.html), leading to a total of 663 matrices of the 12 transition rates. in order to compare results obtained from different pairs, each transition matrix was also normalized and we analyzed […]

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

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