PROGRAM: msa_diff

USAGE: msa_diff [OPTIONS] alignment1.fa alignment2.fa > diffs.out

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.