What is a good phylogenetic tree viewer, such that I can view internal nodes? I have run a script to name internal nodes according to their descendants. My goal is to find internal nodes with homogeneous descendants. I would like to do this by eye but the phylogenetic tree viewers I have tried do not have options, or at the least obvious options, to display these internal node names. I have already tried Mega, Dendroscope, and DNAstar. Any other options?
Alternatively, does anyone have a good script to collapse a large (N>1500) tree according to the leaves naming scheme? My end goal is to cluster the tree as best as possible automatically. Thank you.