mredfar <marhat <at> gmail.com> writes: > > 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 >
I would strongly recommend that you forward this question to the r-sig-phylo <at> r-project.org mailing list, where there are many more people who can answer questions about phylogenetic analysis in R. It's a very friendly list. I was going to suggest you read vignette("Ancestral"), which is mentioned in ?ancestral.par, but it actually doesn't contain the information you're interested in. good luck, Ben Bolker ______________________________________________ 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.