Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff phylogenies/phylobayes33_wrapper.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylogenies/phylobayes33_wrapper.xml Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,53 @@ +<tool id="phylobayes" name="Phylobayes" version="1.0"> + <description>version 3.3b</description> + <requirements> + <requirement type="binary">Phylobayes 3.3b</requirement> + </requirements> + <command interpreter="perl"> +phylobayes33_wrapper.pl $filename $nchain $cycles $discrepancies $effectivesize $burnin $sampleInterval + </command> + <inputs> + <param name="filename" type="data" format="txt" label="Input file (ali)" /> + <param name="nchain" type="integer" value="0" label="Number of chains to run" /> + <param name="cycles" type="integer" value="0" label="Cycle interval to run bpcomp and tracecomp" /> + <param name="discrepancies" type="float" value="0.0" label="Discrepancies ceiling" /> + <param name="effectivesize" type="integer" value="0" label="Effective sizes floor"/> + <param name="burnin" type="integer" value="0" label="Post analysis burnin" /> + <param name="sampleInterval" type="integer" value="0" label="Post analysis sample interval"/> + </inputs> + <outputs> + <data from_work_dir="dataset.con.tre" name="contre" format="txt" /> + <data from_work_dir="dataset.bplist" name="bplist" format="txt" /> + </outputs> + + <help> + +**How it works** +PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. +Compared to other phylogenetic MCMC samplers (e.g. MrBayes ), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. +It is particularly well suited for large multigene alignments, such as those used in phylogenomics. + +The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests, +data recoding (analogous to R/Y coding, but for amino-acids), and cross-validation. It also implements a more efficient tree searching MCMC algorithm. + +http://www.atgc-montpellier.fr/phylobayes/ + +**Citations** +Phylobayes - Bayesian phylogenetic software based on mixture models. + +Lartillot N., Philippe H. "A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process." Molecular Biology and Evolution. 2004 21(6):1095-1109. +http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf + +Lartillot N., Philippe H. "Computing Bayes factors using thermodynamic integration." Systematic Biology. 2006 55:195-207. +http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf + +Lartillot N., Brinkmann H., Philippe H. "Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model." BMC Evolutionary Biology. 2007 Feb 8;7 +Suppl 1:S4. + +This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following. + +Current Osiris Citation is here + +http://osiris-phylogenetics.blogspot.com/2012/10/citation.html + </help> +</tool>