Liam J. Revell wrote on 25/01/2010 05:09:
Hi Sam, Santiago,
To be clear, this procedure yields the "squared-change parsimony"
ancestral states for a continuous character (see Maddison, 1991; Syst.
Zool.). This will not provide MP ancestral state estimates for a
discrete character, if this is what you are looking for.
Note that Maddison (1991) also proposed "weighted squared-change
parsimony" which will provide exactly the same ancestral state estimates
as ML under Brownian motion.
For parsimony reconstruction of discrete characters, there is an
interesting algorithm in:
Narushima, H. and Hanazawa, M. (1997) A more efficient algorithm for MPR
problems in phylogeny. Discrete Applied Mathematics 80:231-238.
I'm planning to have it in ape some time.
Emmanuel
- Liam
Liam J. Revell
NESCent, Duke University
web: http://anolis.oeb.harvard.edu/~liam/
NEW email: lrev...@nescent.org
Samantha Price wrote:
Hi Santiago,
Look at the ace function in the Ape package - to get a max parsimony
reconstruction set branch lengths =1 and run a maximum likelihood
estimation. You can find further information here:
http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction
Sam
On Jan 23, 2010, at 8:32 PM, Santiago Claramunt wrote:
Hi all,
Does anybody know a function in R for performing maximum parsimony
ancestral reconstructions?
Best,
Santiago
Santiago Claramunt
Museum of Natural Science,
119 Foster Hall,
Louisiana State University,
Baton Rouge, LA70803
scla...@tigers.lsu.edu
http://www.museum.lsu.edu/Claramunt/Home.html
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
--
Emmanuel Paradis
IRD, Montpellier, France
ph: +33 (0)4 67 16 64 47
fax: +33 (0)4 67 16 64 40
http://ape.mpl.ird.fr/
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
