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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="tree_support_phyutility" name="tree_support_phyutility">
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2 <description>Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees</description>
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3 <requirements>
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4 <requirement type="package">phyutility</requirement>
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5 </requirements>
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6 <command>
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7 java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/phyutility.jar -ts -in $treesfile -tree $besttree -out $outtree
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8 </command>
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9 <inputs>
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10 <param format="txt" name="treesfile" type="data" label="Input trees file" help="A file of multiple trees in newick format"/>
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11 <param format="txt" name="besttree" type="data" label="Target tree" help="Tree to find support for"/>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="outtree" label="Support by ${tool.name}" />
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15 </outputs>
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16 <help>
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17 **What it does**
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18
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19 Tree support RAxML calculates support values for a given tree using a set of input trees. For example, it can calculate bootstrap support for the ML tree based on a set of trees from a bootstrap analysis.
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20 This is valuable when separating bootstrap analysis from ML analysis, and when separating bootstrap replicates in different runs, which can be concatenated and used as input for this tool.
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21
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22 ------
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23
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24 **Inputs**
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25
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26 1. Tree file with target tree.
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27
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28 2. Set of phylogenies, branch lengths are ignored.
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29
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30 ------
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31
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32 **Outputs**
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33
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34 The focal tree is output with support values in Newick tree format.
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35
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36 -------
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37
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38 **Additional Information**
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39
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40 1. This tool Calls phyutility
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41
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42 2. A similar tool is tree_support_RAxML, which works best with RAxML output
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43
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44 -------
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45
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46 **Citations**
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47
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48 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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49
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50 Current Osiris Citation is here
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51
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52 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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53
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54 Additional Citations for this tool
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55
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56 Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24: 715-716
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57
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58 </help>
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59 </tool>