Tool for mapping homoplasy onto an existing phylogenetic tree

Question

[confusedious]

Hello everyone,

I have a large nucleotide alignment that contains a number of parsimony informative sites that are known to be rapidly evolving and to contain homoplasic characters.

These homoplasic sites were removed for the purposes of phylogenetic reconstruction, but I would now like to map these character changes back onto the tree.

I can do this by hand using parsimony, but I thought there must be a tool out there for doing this kind of thing (doing this manually would take an eternity - there are over 100 taxa in the tree).

Does anyone have a suggestion of a tool that might be useful for this?