alignments-diff - Align two alignments for comparison.

       Benjamin Redelings.

                                                    Feb 2018                                  alignments-diff(1)

       Align two alignments for comparison.

-h, –help
              produce help message

–alphabetarg
              set to `Codons' to prefer codon alphabets

alignments-diff - Align two alignments for comparison.

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

       –dual  Write out the two aligned alignments separately

       –fillarg (=gap)
              blank columns filled with: gap or unknown

       -darg, –differences-filearg
              Filename to store differences in AU format

       –blocksizearg (=20)
              Width of blocks of same color

       –classesarg (=1)
              Number of groups for non-matching characters

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

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

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