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1 <tool id="phylobayes" name="Phylobayes">
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2 <description>Runs phylobayes</description>
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3 <command interpreter="perl">pb.pl $filename $nchain $cycles $discrepancies $effectivesize $burnin $sampleInterval</command>
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4 <inputs>
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5 <param name="filename" type="data" format="txt" label="Input file (ali)" />
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6 <param name="nchain" type="integer" value="0" label="Number of chains to run" />
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7 <param name="cycles" type="integer" value="0" label="Cycle interval to run bpcomp and tracecomp" />
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8 <param name="discrepancies" type="float" value="0.0" label="Discrepancies ceiling" />
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9 <param name="effectivesize" type="integer" value="0" label="Effective sizes floor"/>
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10 <param name="burnin" type="integer" value="0" label="Post analysis burnin" />
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11 <param name="sampleInterval" type="integer" value="0" label="Post analysis sample interval"/>
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12 </inputs>
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13 <outputs>
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14 <data from_work_dir="dataset.con.tre" name="contre" format="txt" />
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15 <data from_work_dir="dataset.bplist" name="bplist" format="txt" />
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16 </outputs>
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17
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18 <help>
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19 Phylobayes - Bayesian phylogenetic software based on mixture models.
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20 Lartillot N., Philippe H. Molecular Biology and Evolution. 2004 21(6):1095-1109.
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21
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22 PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.
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23 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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24 It is particularly well suited for large multigene alignments, such as those used in phylogenomics.
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25
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26 The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests,
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27 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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28
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29 http://www.atgc-montpellier.fr/phylobayes/
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30
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31 "A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process."
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32 http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf
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33 Lartillot N., Philippe H.
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34 Molecular Biology and Evolution. 2004 21(6):1095-1109.
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35
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36 "Computing Bayes factors using thermodynamic integration."
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37 http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf
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38 Lartillot N., Philippe H.
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39 Systematic Biology. 2006 55:195-207.
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40
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41 Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model."
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42 http://www.atgc-montpellier.fr/download/papers/cat_2007.pdf
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43 Lartillot N., Brinkmann H., Philippe H.
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44 BMC Evolutionary Biology. 2007 Feb 8;7 Suppl 1:S4.
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45
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46 "Phylogenomics."
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47 http://www.atgc-montpellier.fr/download/papers/phylogenomics_2005.pdf
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48 Philippe H., Delsuc F., Brinkmann H., Lartillot N.
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49 Annual Review of Ecology, Evolution and Systematics. 2005 36,541-562.
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50
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51 </help>
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52 </tool>
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