[R-sig-phylo] Estimating branch lengths on a fixed topology from molecular data

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

Re: [R-sig-phylo] Estimating branch lengths on a fixed topology from molecular data

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)