R help - Feb 2012 - help with ancestral.pars in phangorn package

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

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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