Phylomatic (Part of Phylocom)


http://www.phylodiversity.net/phylomatic/phylomatic.html
	
	

"The online software 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. 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. 
	
Currently, species are not included in the megatree, and species within a genus are always returned as polytomies.
	(http://www.phylodiversity.net/phylomatic/phylomatic_old.html)
"	
http://bioinformatics.oxfordjournals.org/content/24/18/2098
	

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.


Galaxy and Perl wrapper tool implemented by: Roger Ngo and Todd H. Oakley, UCSB

Included in this package:

* phylomatic - binary file
* phylomatic.pl - wrapper perl script for Galaxy
* phylomatic.xml - Galaxy tool file
* phylomatic_README.txt - documentation file

Installation instruction:

1. Copy the phylomatic binary file to the /bin/ directory of your Galaxy
user account.

2. Copy phylomatic.pl and phylomatic.xml to a folder in the /galaxy-dist/tools/
directory.

3. Add the XML information in tool_conf.xml in /galaxy-dist/

4. Restart Galaxy using:

./run.sh --stop-daemon
./run.sh --reload --daemon

Known Issues:
Since Galaxy will throw STDERR on warnings generated by programs, the Perl wrappper
script is used to redirect any warnings generated by the binary file to a log file.