Mercurial > repos > ucsb-phylogenetics > ucsb_phylogenetics
comparison phylomatic/phylomatic.xml @ 2:4de3f9572615 draft
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| author | ucsb-phylogenetics |
|---|---|
| date | Thu, 21 Jun 2012 17:46:55 -0400 |
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| 1:de3ada25282e | 2:4de3f9572615 |
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| 1 <tool id="phylomatic" name="Phylomatic"> | |
| 2 <description>Run Phylomatic</description> | |
| 3 <command interpreter="perl">./phylomatic.pl $input1 $input2</command> | |
| 4 <inputs> | |
| 5 <param name="input1" type="data" format="txt" label="Phylogenetic Tree" /> | |
| 6 <param name="input2" type="data" format="txt" label="Taxonomy File" /> | |
| 7 </inputs> | |
| 8 | |
| 9 <outputs> | |
| 10 <data from_work_dir="output.txt"/> | |
| 11 </outputs> | |
| 12 | |
| 13 <help> | |
| 14 Phylomatic (Part of Phylocom) | |
| 15 | |
| 16 http://www.phylodiversity.net/phylomatic/phylomatic.html | |
| 17 | |
| 18 The online software takes your list of taxa, and first tries to match them by genus name to the megatree. | |
| 19 Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. | |
| 20 If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. | |
| 21 Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. | |
| 22 (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) | |
| 23 | |
| 24 http://bioinformatics.oxfordjournals.org/content/24/18/2098 | |
| 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. | |
| 26 | |
| 27 </help> | |
| 28 </tool> | |
| 29 |