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1 Phylobayes Galaxy Installation and Configuration Instructions
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2
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3 Phylobayes original binaries written by: Lartillot N., Philippe H. Molecular Biology and Evolution
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4
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5 Galaxy and Perl wrapper script written by: Roger Ngo and Todd H. Oakley, UCSB
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6
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7
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8 Phylobayes - Bayesian phylogenetic software based on mixture models.
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9 Lartillot N., Philippe H. Molecular Biology and Evolution. 2004 21(6):1095-1109.
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10
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11 PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.
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12 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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13 It is particularly well suited for large multigene alignments, such as those used in phylogenomics.
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14
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15 The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests,
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16 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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17
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18 http://www.atgc-montpellier.fr/phylobayes/
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19
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20 "A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process."
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21 http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf
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22 Lartillot N., Philippe H.
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23 Molecular Biology and Evolution. 2004 21(6):1095-1109.
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24
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25 "Computing Bayes factors using thermodynamic integration."
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26 http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf
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27 Lartillot N., Philippe H.
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28 Systematic Biology. 2006 55:195-207.
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29
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30 Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model."
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31 http://www.atgc-montpellier.fr/download/papers/cat_2007.pdf
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32 Lartillot N., Brinkmann H., Philippe H.
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33 BMC Evolutionary Biology. 2007 Feb 8;7 Suppl 1:S4.
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34
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35 "Phylogenomics."
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36 http://www.atgc-montpellier.fr/download/papers/phylogenomics_2005.pdf
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37 Philippe H., Delsuc F., Brinkmann H., Lartillot N.
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38 Annual Review of Ecology, Evolution and Systematics. 2005 36,541-562.
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39
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40
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41
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42 Included in this package:
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43
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44 * pb.pl - Perl wrapper script for the Galaxy tool
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45 * pb.xml - Galaxy Phylobayes XML file
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46 * phylobayes_README - Documentation file
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47
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48 Dependencies: PHYLOBAYES 3.3b must be installed on the Galaxy user account.
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49
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50 How to install Phylobayes
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51
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52 1. Ensure phylobayes 3.3b is installed.
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53
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54 2. Modify the $phylobayes_path and $readPB_path to reflect the location
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55 of pb and readpb in your user account. The default is listed below:
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56
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57 my $phylobayes_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/pb';
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58 my $readPB_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/readpb';
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59
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60 3. Copy pb.pl and pb.xml to a folder in the /galaxy-dist/tools directory.
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61
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62 4. Add the XML tool into the tool_conf.xml file in galaxy-dist/
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63
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64 5. Restart Galaxy with:
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65
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66 ./run.sh --stop-daemon
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67
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68 and then
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69
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70 ./run.sh --reload --daemon |
