[R] help with ancestral.pars in phangorn package

mredfar marhat at gmail.com
Thu Feb 16 09:22:19 CET 2012

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.


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