I made a Principal Coordinate Analysis using the package ape in R, giving as input a pairwise phylogenetic distance matrix of my the samples. I was wondering if it possible to get a hierarchical clustering analyses like for the PCA, in a way to detect clusters on the plot. And if it is possible with program/function should I use.
If I understood your question right, you can use any clustering method (supervised or unsupervised, upon your choice) on principal coordinates . They are given in the compenent 'vectors' in pcoa.
Have you tried princomp() and hclust()? Read more at the Cluster Analysis task view, linked here.
http://cran.r-project.org/web/views/Cluster.html
You can use python orange data mining software
Workflow:
Csc file import->Distances->Hierarchical Clustering
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