[Mesquitelist] Consensus trees and bootstrapping

[Wayne Maddison]

At 12:57 AM -0500 27.5.2008, Lauren Cole Sallan wrote:
>Hello everyone,
>
>I used mesquite to create parsimonious trees from continuous data 
>using the built-in heuristic search.

Please remember that Mesquite's heuristic search does not adjust 
branch lengths, which would be desirable when using continuous data. 
You might want to look into PHYLIP's CONTML as an alternative for 
tree searches.

>Is there any way to obtain a majority rules or strict consensus tree 
>in Mesquite or one of the modules?

Consensus trees can be done using the modules of TreeSetViz, but 
TreeSetViz unfortunately does not work yet with version 2 of 
Mesquite.  We are about to release version 2.5 of Mesquite, and this 
will have built in support for consensus trees.

>Also, is there a way to transfer this treeset and data to Paup or 
>another program in order to run bootstrapping or obtain descriptive 
>stats (CI, RI, RC)? Or is there a way to do this in Mesquite as well?

CI/RI/RC are not available in Mesquite.  To export trees to a file 
there are several methods, including using

-- File>Export, Export Nexus Tree File (or one of the other tree file options)
-- Taxa & Trees>Save Copy of Tree Bock

Wayne

>
>Thanks in advance,
>Lauren
>
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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

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