[R] help with ancestral.pars in phangorn package

Ben Bolker bbolker at gmail.com
Fri Feb 17 14:29:24 CET 2012

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

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