NAME

       alignments-diff - Align two alignments for comparison.

SYNOPSIS

       alignments-diff alignment-file1 alignment-file2 [OPTIONS]

DESCRIPTION

       Align two alignments for comparison.

GENERAL OPTIONS:

       -h, --help
              produce help message

INPUT OPTIONS:

       --alphabet arg
              set to 'Codons' to prefer codon alphabets

OUTPUT OPTIONS:

       --merge
              Stack the two alignments into one alignment with duplicate names

       --dual Write out the two aligned alignments separately

       --fill arg (=gap)
              blank columns filled with: gap or unknown

       -d arg, --differences-file arg
              Filename to store differences in AU format

       --blocksize arg (=20)
              Width of blocks of same color

       --classes arg (=1)
              Number of groups for non-matching characters

REPORTING BUGS:

       BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

       Please send bug reports to <bali-phy-users@googlegroups.com>.

AUTHORS

       Benjamin Redelings.

                                             Feb 2018                          alignments-diff(1)