Mercurial > repos > ucsb-phylogenetics > ucsb_phylogenetics
comparison phylomatic/phylomatic_README.txt @ 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 Phylomatic (Part of Phylocom) | |
| 2 | |
| 3 | |
| 4 http://www.phylodiversity.net/phylomatic/phylomatic.html | |
| 5 | |
| 6 | |
| 7 | |
| 8 "The online software takes your list of taxa, and first tries to match them by genus name to the megatree. | |
| 9 | |
| 10 Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. | |
| 11 | |
| 12 If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. | |
| 13 | |
| 14 Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. | |
| 15 (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) | |
| 16 " | |
| 17 http://bioinformatics.oxfordjournals.org/content/24/18/2098 | |
| 18 | |
| 19 | |
| 20 Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. | |
| 21 Bioinformatics, 24: 2098-2100. | |
| 22 | |
| 23 | |
| 24 Galaxy and Perl wrapper tool implemented by: Roger Ngo and Todd H. Oakley, UCSB | |
| 25 | |
| 26 Included in this package: | |
| 27 | |
| 28 * phylomatic - binary file | |
| 29 * phylomatic.pl - wrapper perl script for Galaxy | |
| 30 * phylomatic.xml - Galaxy tool file | |
| 31 * phylomatic_README.txt - documentation file | |
| 32 | |
| 33 Installation instruction: | |
| 34 | |
| 35 1. Copy the phylomatic binary file to the /bin/ directory of your Galaxy | |
| 36 user account. | |
| 37 | |
| 38 2. Copy phylomatic.pl and phylomatic.xml to a folder in the /galaxy-dist/tools/ | |
| 39 directory. | |
| 40 | |
| 41 3. Add the XML information in tool_conf.xml in /galaxy-dist/ | |
| 42 | |
| 43 4. Restart Galaxy using: | |
| 44 | |
| 45 ./run.sh --stop-daemon | |
| 46 ./run.sh --reload --daemon | |
| 47 | |
| 48 Known Issues: | |
| 49 Since Galaxy will throw STDERR on warnings generated by programs, the Perl wrappper | |
| 50 script is used to redirect any warnings generated by the binary file to a log file. |