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annotate phylogenies/phylobayes33_wrapper.xml @ 0:5b9a38ec4a39 draft default tip
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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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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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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> |