I am interested in counting the number of parallel acquisitions of mutations in 
ancestral reconstructions of nucleotide character states on phylogenies.

For example, in the code below (based on the phangorn vignette), the "t" 
nucleotide mutation has occurred on 3  branches and the "a" nucleotide on one.



fdir <- system.file("extdata/trees", package = "phangorn")

primates <- read.phyDat(file.path(fdir, "primates.dna"), format = "phylip")

tree = pratchet(primates, trace=0)

tree = acctran(tree, primates)

#parsimony(tree, primates)

anc.mpr = ancestral.pars(tree, primates, "MPR")

plotAnc(tree, anc.mpr, 15)


In the spirit of not re-inventing the wheel, I wonder if someone else developed 
a method to count these changes? It doesn't necessarily have to be implemented 
using phangorn classes.




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