Hello I have phylogenetic trees of deep sequencing data. The problem is that many of the sequences are identical so i wanted to have those nodes that have x number of identical sequences be represented by a circle of size x. This is easily enough done in R using the APE package. The problem is I have two groups of sequences that I want to color differently. So at node 1 for example, 30% of the identical sequences come from group 1, and 70% come from group 2. Ideally these circles at nodes would actually be pie charts that show the different representation but I cannot figure out how to calculate the vector to feed ape. any ideas?

Thanks, Brendan