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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="phylomatic" name="Phylomatic" version="1.0.1">
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2 <description>Run Phylomatic</description>
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3 <requirements>
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4 <requirement type="binary">Phylocom Phylomatic</requirement>
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5 </requirements>
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6 <command interpreter="perl">./phylomatic.pl $input1 $input2</command>
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7 <inputs>
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8 <param name="input1" type="data" format="txt" label="Phylogenetic Tree" />
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9 <param name="input2" type="data" format="txt" label="Taxonomy File" />
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10 </inputs>
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11
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12 <outputs>
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13 <data from_work_dir="output.txt"/>
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14 </outputs>
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15
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16 <help>
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17 **What it does**
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18
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19 Phylomatic (Webb & Donoghue, 2005) is part of the Phylocom software package (Webb et al., 2008).
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20 Phylomatic takes your list of taxa, and first tries to match them by genus name to the megatree. Failing that, they are attached by family name.
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21 If all the genera appear in the megatree, then that family appears resolved. If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera.
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22 Currently, species are not included in the megatree, and species within a genus are always returned as polytomies.
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23
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24 ------
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25
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26 **Inputs**
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27
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28 Input 1: Phylogeny in Newick format.
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29 Input 2: List of taxa in delimited text file.
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30
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31 ------
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32
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33 **Outputs**
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34
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35 Phylomatic matches input taxa to the most resolved possible position in any of a set of master
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36 trees in the database (the 'megatrees') and returns the phylogeny in one of a variety of formats:
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37 graphical, Newick, NEXUS, or tabular.
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38
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39 -------
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40
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41 **Citations**
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42
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43 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use
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44 of this tool in a publication, please consider citing the following.
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45
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46 Current Osiris Citation is here
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47
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48 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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49
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50 Additional Citations for this tool
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51
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52 Phylomatic (Part of Phylocom software package)
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53
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54 http://phylodiversity.net/phylomatic/html/pm2_form.html
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55
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56 If you use results derived from Phylocom analyses in your publications, please cite:
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57
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58 Webb, C. O., Ackerly, D. D. & Kembel, S. W. 2008. Phylocom: software for the analyses of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2089-2100.
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59 doi: 10.1093/bioinformatics/btn358
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60
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61 Original Phylomatic citation:
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62
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63 Webb, C. O. & Donoghue, M. J. 2005. Phylomatic: tree assembly for applied phylogenetics. Molecular
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64 Ecology Resources, 5: 181-183. doi: 10.1111/j.1471-8286.2004.00829.x
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65 </help>
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66 </tool>
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67