I'm a little new to this, but would much appreciate any help. I have lines of DNA sequence, aligned by the identity of letters within them. I'd like to sum the % identity of each in the sequence, generating a matrix for the entire alignment. i.e. 
fred  ATGTTGTAT
fred1 ATCTTATAT
fred2 ATCTTATAT


A  3 0 0 0 0 2 0 3 0
T  0 3 0 3 3 0 3 0 3
G  0 0 1 0 0 1 0 0 0
C  0 0 2 0 0 0 0 0 0

[download]
This will be for 10K+ sequences though, hence the script requirement. I figure that the best way is to count the incidence of each letter at each position within each line and sum them in the matrix, but I'm yet to work out how to do this. Thoughts would be much obliged... Thanks.

In reply to To count letters (%identity) in DNA alignment by sedm1000

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