NAME

       msa_diff - Compare two multiple alignments and report differences.

DESCRIPTION

       Compare two multiple alignments and report differences.

OPTIONS

       --format1, -i FASTA|SS|PHYLIP|MPM|MAF

              Format of first alignment (default is to guess format from file contents).

       --format2,  -j  FASTA|SS|PHYLIP|MPM|MAF  Format  of  second alignment (default is to guess
              format from file contents).

       --alphabet,  -a  <alphabet_string>  Use  given  string  for  alphabet.   Can  be  used  to
              accommodate

              nonstandard  characters  (e.g., 'b' for any base or '^' for insertion gaps, '.' for
              deletion gaps).

       --ignore-base-id, -b Ignore  identity  of  bases;  consider  all  alphabetical  characters
              equivalent (e.g., A, C, G, T, N, X, b).

       --ignore-gap-type, -g

              Ignore type of gap; consider '-', '^', and '.' all equivalent.

       --help, -h Display this help message and exit.