Dear R-sig phylo list members,
I am trying to apply maximum Parsimony tree searches on a large number of
simulated datasets within the R environment. So far I have found one function
implementing Parsimony: the optim.parsimony function in the package phangorn.
This function finds a shortest
Hi Robin.
Yes, you can do this under the ACCTRAN (accelerated transformation)
criterion using the function acctran() in phangorn. To do this given
a data file sequences.dna in FASTA format:
dna-read.phyDat(sequences.dna,format=fasta)
tree-pratchet(dna) # or you could use optim.parsimony()
