[Mesquitelist] discrepancy in taxa samples

[Wayne Maddison]

You can reconstruct with missing data, but the results are messy -- 
you would have to look at thousands of nodes in the tree to find the 
one you want.

Is there a specific reason you don't want to delete the irrelevant taxa?

You can quickly delete the irrelevant taxa as follows.  Read in the 
tree & matrix.  Go to the matrix editor.  Use the magic wand with a T 
to select all taxa with a ?.  Now hit the delete key to delete all 
taxa with ?.  The taxa will be automatically deleted from the tree. 
Use File>Save as to save the trimmed file.

You can delete the irrelevant taxa from the tree (but not the matrix) 
by selecting all with a ? then going to the tree window and choosing 
"Cut selected taxa".

Does this help?

Wayne


At 4:36 PM +0000 14.11.2009, m. candida wrote:
>I have 8 categorical character states for 134 taxa. The tree I am 
>using (supertree constructed by Bidinda-Edmonds et al, Nature, 2007) 
>has several thousand taxa. Is there a way to use this tree with my 
>data without removing the thousands of irrelevant taxa? I would like 
>to reconstruct ancestral states under parsimony and ML. Any advice 
>would be appreciated.
>
>Regards,
>Therese
>
>
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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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