Dear all, I am looking into the possibilities of ancestral character state reconstruction in R. I would like to reconstruct discrete (ordered) characters using maximum parsimony and maximum likelihood. I have found the 'ace' and 'MPR' functions and ace appears to do what I want.
MPR is giving me issues, however, because of the requirement of specifying a single outgroup. My input tree is already rooted, but the 'outgroup' is a clade rather than a single terminal. Therefore, specifying a single outgroup terminal is impractical. Do you know if there is a workaround so that I can use MPR on a rooted tree directly? Or do you know another function for ancestral character state reconstruction under maximum parsimony? Thanks in advance for your advice, Best wishes, Robin van Velzen Wageningen University _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
