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2
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1 <tool id="phylomatic" name="Phylomatic">
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2 <description>Run Phylomatic</description>
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3 <command interpreter="perl">./phylomatic.pl $input1 $input2</command>
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4 <inputs>
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5 <param name="input1" type="data" format="txt" label="Phylogenetic Tree" />
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6 <param name="input2" type="data" format="txt" label="Taxonomy File" />
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7 </inputs>
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8
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9 <outputs>
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10 <data from_work_dir="output.txt"/>
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11 </outputs>
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12
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13 <help>
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14 Phylomatic (Part of Phylocom)
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15
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16 http://www.phylodiversity.net/phylomatic/phylomatic.html
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17
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18 The online software takes your list of taxa, and first tries to match them by genus name to the megatree.
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19 Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved.
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20 If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera.
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21 Currently, species are not included in the megatree, and species within a genus are always returned as polytomies.
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22 (http://www.phylodiversity.net/phylomatic/phylomatic_old.html)
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23
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24 http://bioinformatics.oxfordjournals.org/content/24/18/2098
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25 Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2098-2100.
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26
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27 </help>
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28 </tool>
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29
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