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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="phylobayes" name="Phylobayes" version="1.0">
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2 <description>version 3.3b</description>
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3 <requirements>
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4 <requirement type="binary">Phylobayes 3.3b</requirement>
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5 </requirements>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 <command interpreter="perl">
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7 phylobayes33_wrapper.pl $filename $nchain $cycles $discrepancies $effectivesize $burnin $sampleInterval
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8 </command>
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9 <inputs>
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10 <param name="filename" type="data" format="txt" label="Input file (ali)" />
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11 <param name="nchain" type="integer" value="0" label="Number of chains to run" />
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12 <param name="cycles" type="integer" value="0" label="Cycle interval to run bpcomp and tracecomp" />
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13 <param name="discrepancies" type="float" value="0.0" label="Discrepancies ceiling" />
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14 <param name="effectivesize" type="integer" value="0" label="Effective sizes floor"/>
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15 <param name="burnin" type="integer" value="0" label="Post analysis burnin" />
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16 <param name="sampleInterval" type="integer" value="0" label="Post analysis sample interval"/>
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17 </inputs>
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18 <outputs>
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19 <data from_work_dir="dataset.con.tre" name="contre" format="txt" />
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20 <data from_work_dir="dataset.bplist" name="bplist" format="txt" />
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21 </outputs>
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22
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23 <help>
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24
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25 **How it works**
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26 PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.
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27 Compared to other phylogenetic MCMC samplers (e.g. MrBayes ), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT.
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28 It is particularly well suited for large multigene alignments, such as those used in phylogenomics.
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29
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30 The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests,
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31 data recoding (analogous to R/Y coding, but for amino-acids), and cross-validation. It also implements a more efficient tree searching MCMC algorithm.
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32
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33 http://www.atgc-montpellier.fr/phylobayes/
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34
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35 **Citations**
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36 Phylobayes - Bayesian phylogenetic software based on mixture models.
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37
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38 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.
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39 http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf
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40
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41 Lartillot N., Philippe H. "Computing Bayes factors using thermodynamic integration." Systematic Biology. 2006 55:195-207.
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42 http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf
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43
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44 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
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45 Suppl 1:S4.
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46
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47 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.
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48
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49 Current Osiris Citation is here
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50
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51 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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52 </help>
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53 </tool>