[Mesquitelist] acctran/deltran

[Wayne Maddison]

No, Mesquite does not have the option to use ACCTRAN.  By default (as 
was the case with MacClade) it shows all most parsimonious states at 
each node.  ACCTRAN would attempt to resolve ambiguities in ancestral 
state reconstructions so as to maximize reversals, although it often 
can't yield full resolution unless arbitrary choices are made.

Mesquite has a method to resolve ambiguities, but instead of choosing 
one resolution that maximizes reversals, it permits you to see each 
of the many possible resolutions.  This is the MPRs mode.

If you need to use ACCTRAN, it's implemented in MacClade.  MacClade 
won't necessarily give a completely resolved reconstruction, however, 
because that would require (in some cases) arbitrary choices.

Wayne


At 7:12 PM -0600 29.12.2009, Joshua M. Brokaw wrote:
>Hi,
>
>I would like a confirmation that the parsimony-based, discrete 
>ancestral state reconstructions in Mesquite use acctran 
>optimizations.  It would be great if the manual mentioned this in the 
>future also.
>
>Thanks,
>
>Joshua M. Brokaw, Ph.D.
>Assistant Professor
>Department of Biology
>Abilene Christian University
>ACU Box 27868
>Abilene, Texas 79699-7868
>325-674-2168
>fax 325-674-2009
>josh.brokaw at acu.edu
>
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>Mesquitelist at mesquiteproject.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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