Mercurial > repos > ucsb-phylogenetics > ucsb_phylogenetics
diff pb.xml @ 0:bbf0d9e9b82a draft
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author | ucsb-phylogenetics |
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date | Thu, 31 May 2012 19:44:16 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pb.xml Thu May 31 19:44:16 2012 -0400 @@ -0,0 +1,52 @@ +<tool id="phylobayes" name="Phylobayes"> + <description>Runs phylobayes</description> + <command interpreter="perl">pb.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> + Phylobayes - Bayesian phylogenetic software based on mixture models. + Lartillot N., Philippe H. Molecular Biology and Evolution. 2004 21(6):1095-1109. + + 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/ + + "A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process." + http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf + Lartillot N., Philippe H. + Molecular Biology and Evolution. 2004 21(6):1095-1109. + + "Computing Bayes factors using thermodynamic integration." + http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf + Lartillot N., Philippe H. + Systematic Biology. 2006 55:195-207. + + Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model." + http://www.atgc-montpellier.fr/download/papers/cat_2007.pdf + Lartillot N., Brinkmann H., Philippe H. + BMC Evolutionary Biology. 2007 Feb 8;7 Suppl 1:S4. + + "Phylogenomics." + http://www.atgc-montpellier.fr/download/papers/phylogenomics_2005.pdf + Philippe H., Delsuc F., Brinkmann H., Lartillot N. + Annual Review of Ecology, Evolution and Systematics. 2005 36,541-562. + + </help> +</tool>