[phylocom-user] Taxa file

Ken Whitney kwhitney at rice.edu
Thu Nov 5 12:19:15 PST 2009


Hi Steve,

Thanks for the quick reply. 

Sorry to be dense about this.  We have working phylo and sample files 
that produce good output (e.g. in Comstruct).  As far as we can tell, 
our traits file is as it should be (and we have checked that the taxa 
match between files, etc.).  So when we couldn't get Comtrait to run 
using these files, we went back to the traits and sample files from 
/example_data files.  At first, Comtrait would not run on those either, 
but when the Taxa file was added back into the folder (it had been 
missing) they ran.  That's why we assumed it was needed. 

I just tried to run Comtrait again without a taxa file in the folder and 
I get the error "Cannot find file: taxa" with no output.

Thanks again,
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/



Steven Kembel wrote:
> 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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>>
>
>
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