Hi all,
I am interested in finding homoplasious sites in a nucleotide sequence
alignment on a ML tree calculated from that alignment. Is there a commonly
used approach for doing this in ape, phangorn etc. I have tried a number of
google searches based around 'R homoplasy' but cant find anything.
On a related note, is there a function available to calculate the consistency
index for a given position on an alignment rather than an average for the whole
alignment, which is what CI in phangorn does now?
thanks!
Tim
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