[Mesquitelist] Tree sample manipulation

[Joseph W. Brown]

I was using the 'Include' approach, but my problem was that my tree  
log file contained both a Taxa block and a Translate block - deleting  
taxa from one block left my trees unaltered, but deleting them from  
the other block pruned the taxa from the trees as I had hoped.

Thanks for the assistance.
Joseph.

On 25 May., 2009, at 11:52 , Wayne Maddison wrote:

> Mesquite has two ways to read tree files.  (1) Using Include or Link  
> file, or Import File With Trees, Mesquite reads in all the trees  
> into memory at once.  When Mesquite does this, and you delete taxa,  
> the trees can be resaved with these taxa deleted. (2) Using Use  
> Trees from Separate Nexus File, or Sample Trees from Separate Nexus  
> File, or MrBayes Trees from .t File, Mesquite reads in the trees  
> only one at a time, and leaves the remaining trees on disk, not in  
> memory.  In this second mode, the external tree file is treated as  
> "read-only". If you delete taxa in the matrix, Mesquite doesn't go  
> through the external tree file and delete those taxa from all the  
> trees.
>
> I assume you read the trees from MrBayes using the second mode?
>
> You could read in the file using the first mode, but perhaps there  
> are too many trees to hold in memory all at once.
>
> We will look into the possibility of simple transforming module that  
> takes trees from one tree file, transforms them, and writes them  
> straight into another file.  This would be a useful module.
>
> Wayne
>
>
> At 8:36 AM -0400 24.5.2009, Joseph Warren Brown wrote:
>> Y'All,
>>
>> I have a tree sample log file (from MrBayes) containing X trees for  
>> N taxa. I want to remove Y taxa (e.g. outgroup) from each tree and  
>> re-save the log file (i.e. X trees with N-Y taxa). I can  
>> successfully load the trees and the character matrix in Mesquite,  
>> as well as define the relevant taxon groups. However, when I try to  
>> delete the taxa they are only remove from the character matrix.
>>
>> Suggestions are appreciated.
>>
>> Thanks.
>> Joseph.
>> ______________________________________________________________
>> Joseph W. Brown, PhD Candidate
>> Museum of Zoology, Bird Division
>> 3015 Ruthven Museums Building
>> 1109 Geddes Avenue
>> University of Michigan, Ann Arbor MI 48109-1079
>> Fax: (734) 763-4080
>> Email: josephwb at umich.edu
>> Homepage: http://www.umich.edu/~josephwb/
>> Family page: http://goghbirth.blogspot.com/
>> Calliope's page: http://calliopessnapshots.blogspot.com/
>>
>>
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>
>
> -- 
> --------------------------------------------------------
> Wayne Maddison
> Professor and Canada Research Chair
>         Depts. of Zoology and Botany and
>         Biodiversity Research Centre
> & Director
>         Beaty Biodiversity Museum
> 6270 University Boulevard
> University of British Columbia
> Vancouver, BC  V6T 1Z4   Canada
>
> email: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416
>
> Mesquite: http://mesquiteproject.org
> MacClade: http://macclade.org
> Salticidae:  http://salticidae.org
> Tree of Life: http://tolweb.org
> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
> Home page: http://salticidae.org/wpm/home.html
>
>



______________________________________________________________________________________________
Joseph W. Brown, PhD Candidate
Museum of Zoology, Bird Division
3015 Ruthven Museums Building
1109 Geddes Avenue
University of Michigan, Ann Arbor MI 48109-1079
Fax: (734) 763-4080
Email: josephwb at umich.edu
Homepage: http://www.umich.edu/~josephwb/
Biology 162 Laboratory: http://www-personal.umich.edu/~josephwb/Biol162/Lab.html
Tree of Life Web Project (Neornithes): http://tolweb.org/tree?group=Neornithes&contgroup=Aves
Family page: http://goghbirth.blogspot.com/
Calliope's page: http://calliopessnapshots.blogspot.com/