[phylocom-user] Taxa file

Steven Kembel steve.kembel at gmail.com
Thu Nov 5 10:32:16 PST 2009


Hi Ken,

comtrait requires two files to run - a sample file that contains  
information on the communities, and a traits file that contains  
information on the traits of the taxa in those communities. There are  
examples of both formats included in the /example_data directory of  
Phylocom 4.1 (named sample and traits, respectively). Please have a  
look at those for an example of how the files need to be formatted, as  
well as page 8 of the Phylocom manual where the format of these two  
files are defined. There is also a tutorial linked to from the  
Phylocom homepage that goes through the process of running the  
comtrait function:

http://bodegaphylo.wikispot.org/Community_Phylogenetics

Cheers,
Steve

On Nov 5, 2009, at 9:42 AM, Ken Whitney wrote:

> Hello all,
>
> We kept crashing Phylocom trying to run Comtrait before finally  
> realizing that it won't run without a Taxa file.  I hope we didn't  
> miss it, but we can't find any information in the manual on what the  
> Taxa file is/contains, and it is not obvious from looking at the  
> example Taxa file provided.  Hints?
>
> Many thanks,
> Ken
>
> -- 
> ------------------
> Ken Whitney
> Assistant Professor
> Dept. of Ecology and Evolutionary Biology
> Rice University
> Houston, TX 77005 USA
> 713 348 3057
> http://www.ruf.rice.edu/~kwhitney/
>
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> phylocom-user at lists.phylodiversity.net
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