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.

msa_diff 1.4                                        May 2016                                         MSA_DIFF(1)