I'm wondering if anyone knows any tools which allow me to count the frequency of amino acids at any specific position in a multiple-sequence alignment.
For example if I had three sequences:
Species 1 - MMRSA Species 2 - MMLSA Species 3 - MMRTA
I'd like for a way to search by position for the following output:
Position 1 - M = 3; Position 2 - M = 3; Position 3 - R = 2, L = 1; Position 4 - S = 2, T = 1; Position 5 - A = 3.
Thanks! I'm familiar with R and Linux, but if there's any other software that can do this I'm sure I can learn.