[Mesquitelist] How does one view multiple "traced" trees without redoing ancestral state reconstructions each time?

[Wayne Maddison]

I'll need more specifics as to what you're doing, because under the 
most obvious scenario Mesquite wouldn't (or shouldn't) retrace for 
all trees.  So first I need to make sure I understand what you're 
doing.  Do you have a tree window open, showing one of the 1000 
trees, and you have Trace Character History on?  If so, then when you 
scroll to a new tree, it should just recalculate ancestral states on 
that one tree.

When you say that it redoes the analysis across all trees every time, 
how do you know it is doing that?

Is it possible you have a chart window open that depends on the tree 
in the tree window (e.g. by providing simulated characters?) and this 
is what is being recalculated?

Wayne


At 10:19 AM -0500 23.2.2009, Marc Johnson wrote:
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>Content-language: en-us
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>
>Dear Mesquite users:
>
>I am performing ancestral state reconstructions of a binary 
>character on a sample of Bayesian trees (1000) using maximum 
>parsimony and BiSSE.
>
>For the MP analyses I am interested in looking at each tree to see 
>how many times MP identifies the state change having occurred  in 
>one direction (0 to 1) versus the reverse direction (1 to 0). When I 
>try and scroll between trees Mesquite retraces the ancestral state 
>across each of the 1000 trees.
>
>Is there a way to view or print the MP ancestral state 
>reconstruction of each tree without redoing the analysis across all 
>trees every time?
>
>I have had similar issues with BiSSE, but those analyses it is 
>possible to work around the problem by outputting the ML estimates 
>to a text file.
>
>Any suggestions would be greatly appreciated.
>
>Marc
>
>
>****************************
>Marc Johnson, Ph.D.
>Assistant Professor
>Department of Plant Biology
>North Carolina State University
>Box 7612, Raleigh NC 27695 U.S.A.
>Phone: 919-515-0478, Fax: 515-3436
>www.evoeco.org
>****************************
>
>
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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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