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
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)