Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output.
The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matrix columns represent the four nucleotide states a, c, g, t, but what I'm unclear about is what the rows represent, and what do the row names mean, the seem to be powers of 2, (1,2,4,8) etc, do these represent reconstruction uncertainties?? Also if you have any advice on how to extract a "change list" from this ancestral.pars output, (ie a list of character changes at each variable site in the sequence and in which nodes/organisms) I would be very thankful. Maha -- View this message in context: http://r.789695.n4.nabble.com/help-with-ancestral-pars-in-phangorn-package-tp4393260p4393260.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
