I could make a python script to do this for me but I'd rather be lazy and use a tool if it already exists.
What I want to do is enumerate the various amino acid mutations at each position of a multiple sequence alignment.
E.G. the first sequence is the reference.
>seq1 AABA-DC >seq2 BABBCDD >seq3 -ABBADD
Position 1: B,1; -,1; Position 4: B,2; Position 5: C,1; A, 1; Position 6: D, 2;
A Soggy Waffle