[Mesquitelist] Simulated and ancestral states

[Wayne Maddison]

As you note, there is an alternative source of character histories 
when you are tracing individual character histories.  You aren't 
asked about this initially, but after Trace Character History is 
running, go to the Trace menu and choose Character History 
Source>Simulate Ancestral States.  This assigns to the nodes the 
actual ancestral states as they happened in the simulation.

But you want it for a matrix.  You can get this done automatically 
using scripting (scrolling from character to character, for each 
recording the ancestral states to a file), but the output would not 
be a simple table that would be easy to read into Excel.  Exactly how 
would you hope to visualize or summarize this?

If you want me to explain how to save output for 1000 characters in a 
script, I could send it to the list.

Wayne


At 6:02 PM +0200 6.6.2007, Michel Laurin wrote:
>Hello fellow Mesquite users,
>
>	I have simulated 1000 continuous characters over a tree using 
>the Brownian motion algorithm and reconstructed its ancestral states 
>in Mesquite. I would like to know its simulated (real) ancestral 
>states. I know that this is possible in Mesquite character by 
>character by reusing the same seed number. But is it possible for a 
>whole matrix? I don't want to do this 1000 times... I think that I 
>had asked Wayne a couple years ago this question, and then, I think 
>this was not possible, but perhaps it now is. Thanks.
>
>	Michel
>--
>Michel Laurin
>CNRS UMR 7179
>Université Paris 6 - Pierre et Marie Curie
>2, place Jussieu
>case 7077
>75005 Paris
>FRANCE
>
>tel. (33 1) 44 27 36 92
>http://tolweb.org/notes/?note_id=3669
>
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-- 
--------------------------------------------------------
Wayne Maddison                    
  Professor and Canada Research Chair
  Departments of Zoology and Botany
    and Centre for Biodiversity Research
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wmaddisn at interchange.ubc.ca   FAX: (604) 822-2416

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