Hello Alejandro,
you can use the phangorn package to do this in R.
The code could look like this:
library(phangorn)
tree - read.tree(treefile) # load the tree / topology
dat - read.phyDat(datafile) # load the data
#Parsimony, apply length using the ACCTRAN criterion
treeMP - acctran(tree, data)
plot(treeMP)
# ML
fit - pml(tree, data) # set up a ML object
fit - optim.pml(fit) # optimise edge lengths
treeML - fit$tree
plot(treeML)
Regards,
Klaus
On 2/3/12, Alejandro Gonzalez V alejandro.gonza...@ebd.csic.es wrote:
Hello,
I was wondering if it is possible to estimate branch lengths on a fixed
topology from a matrix of nuclear or mitochondrial DNA data. I used to do
this in PAUP and would very much like to have an alternative in R. In PAUP
one loaded a matrix of molecular data and a topology (without branch
lengths) with identical species coverage, then branch lengths were estimated
using maximum likelihood (could also use parsimony) and given settings for
the substitution model.
Any tips would be appreciated!
Best wishes
Alejandro
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Alejandro Gonzalez Voyer
Post-doc
Estación Biológica de Doñana (CSIC)
Avenida Américo Vespucio s/n
41092 Sevilla
Spain
Tel: +34- 954 466700, ext 1749
E-mail: alejandro.gonza...@ebd.csic.es
Web-site (Under Construction):
Group page: http://consevol.org/index.html
Personal web-page: http://consevol.org/members/alejandro.html
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