[Mesquitelist] summarize state changes

[Wayne Maddison]

All ancestral state reconstruction methods in Mesquite use information over the whole tree, even if they report results just for specific clades or branches.

When used with likelihood with modes that have some parameters unspecified (and hence in need of estimation), Summarize State Changes Over Trees does the parameter estimates separately for each character -- i.e. they don't use a single model for the whole matrix.

If you can find a small matrix (with just one or a few characters) that seems to show very unusual numbers of transformations, could you send me the file so I can see if it's behaving correctly?

You're correct, this menu item has moved to Analysis>Other.

Wayne


On 29 Nov 2010, at 7:17 PM, Hearn, David J. wrote:

> 
> Hi folks,
> 
> Quick questions... sorry if the answers are already documented somewhere, but I can't find them.
> 
> What menu path will get me to 'Summarize State Changes Over Trees' for entire trees (not sub-clades), with character model parameters estimated at the same time? Online documentation suggests looking in the Taxa&Trees menu, but I don't see it there. It is in the Analysis->Other->Summarize State Changes Over Trees, but I am wondering if the character state reconstructions are based on the entire tree or a sub-clade. Previous attempts resulted in the inference of very unusual numbers of character transformations. Perhaps it is a Mesquite version issue? I downloaded version 2.74 (build 550), but 'Summarize State Changes Over Trees' is not in the Taxa&Trees menu in this version either.
> 
> Thanks for your help.
> 
> Cheers,
> David
> 
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--------------
Wayne Maddison
    Professor and Canada Research Chair, Depts. of Zoology and Botany
    & Director, Beaty Biodiversity Museum
6270 University Boulevard
University of British Columbia
Vancouver, BC  V6T 1Z4   Canada

Home page: http://salticidae.org/wpm/home.html
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Beaty Biodiversity Museum: http://beatymuseum.ubc.ca