Hi Santiago,
it is possible to extract the information for the root for the sankoff
algorithm in the phangorn package (this is for discrete characters).
I'll added a function called pace, which will do the job. Of course
maximum parsimony will not provide unique solutions, but several
characters c
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
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 Maddiso
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
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.h
