alignments-diff(1)

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.