marjon van dijk wrote:
> Given a multiple alignment of ten mammal sequences, is it possible to judge
> objectively that two mammals with the same amino acid on one site and the
> other eight mammals having another amino acid on this site have a shared
> derived character or that it is homoplasy? So, are there methods to
> calculate the rate of homoplasy for each site in the alignment?
There is one method for doing this. see
Meacham(1994) Sys. Bot. 19:506-522. where he described his character
As far as I have seen, attempts to model homoplasy using stochastic
models have not created very realistic data sets.