I have a bunch of SNP-matrices as aligned nucleotide sequences and have no issues in making all kinds of trees out of the alignment. However, I can not find any tool that can plot the actual nucleotide changes (character state changes, mutations) on the branches. I am dreaming of a tool that can take my .fasta (or .phy) alignment, extract the different states at all positions and plot them on a tree in a "[char_nr]: [change from]>[change to]" way (eg: 12: A>C) or similar to that.
I have tried with the most common classic phylo packages (MEGA7, PAUP4, Mesquite) and also with ETE 3 (python), but all without success (I can get a list of changes and the changes for a single character in PAUP and MEGA, but I am not able to get the information on one tree). MacClade should be able to do that, but I have no access to a PowerPC-Mac which could run the old code. And WinClada, besides that I don't like spending $50 for trying something, has their servers down at the moment, so no access.
Does anybody have experience with that and can help me out? Thank you so much in advance!