[Mesquitelist] Tree sample manipulation

[Wayne Maddison]

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

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