[Taxacom] Character transformation series on maximum, likelihood and 'Bayesian' trees

[Sergio Vargas]

  Hi

very interesting question. I'm almost sure PAUP's RECONSTRUCT will only 
show the ancestral sequence and not the substitution process leading to 
the next node/tip. If reconstructed under Maximum Likelihood (ML), I 
guess it will show you the ancestral sequence with the maximum 
likelihood, and this, I assume, will be done traversing the tree and 
calculating the most likely base for site S at each node in the tree 
until reaching the root (i.e. using Felsenstein pruning algorithm or 
some variation of it). I think you can do what you want in PAML using 
baseml, at least in the paper describing the method they talk about 
mutation paths. Don't know about MrBayes but the methods doesn't seem to 
give info on the paths.

hope it helps

sergio

On 7/16/11 7:00 PM, taxacom-request at mailman.nhm.ku.edu wrote:
> Message: 3
> Date: Fri, 15 Jul 2011 14:12:09 -0700
> From: "J. Kirk Fitzhugh"<kfitzhugh at nhm.org>
> Subject: [Taxacom] Character transformation series on maximum
> 	likelihood and 'Bayesian' trees
> To: TAXACOM<taxacom at mailman.nhm.ku.edu>
> Message-ID:<4E20AD29.7030804 at nhm.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Do phylogenetics programs that perform maximum likelihood or Bayesian
> analyses allow for indicating character state changes on resultant trees
> in the same way as is done with parsimony? More specifically, if a
> resultant tree has 'long branches,' can all state changes indicating
> that length be shown on a tree? PAUP* has a 'reconstruct' command that
> the manual says can be used for both parsimony- and likelihood-derived
> trees, but I'm curious if anyone has experience with the latter and if
> multiple state changes associated with long branches are actually mapped
> onto the tree.
>
> Thanks,
> Kirk
>
> -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ J. Kirk Fitzhugh, Ph.D. 
> Curator of Polychaetes Invertebrate Zoology Section Research& 
> Collections Branch Natural History Museum of Los Angeles County 900 
> Exposition Blvd Los Angeles CA 90007 Phone: 213-763-3233 FAX: 
> 213-746-2999 e-mail: kfitzhug at nhm.org 
> http://www.nhm.org/site/research-collections/polychaetous-annelids


-- 
Sergio Vargas R., M.Sc.
Molecular Geo- and Palaeobiology Lab.
Dept. of Geo-&  Environmental Sciences, Palaeontology and Geobiology
LMU München
Richard-Wagner Str. 10
80333 Munich, Germany
tel. +49 89 2180 17929
s.vargas at lrz.uni-muenchen.de
sergio.vargasr at ecci.ucr.ac.cr

check my webpage:
https://sites.google.com/site/marinemolecularevolution/

check my research ID:
http://www.researcherid.com/rid/A-5678-2011