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

REPORTING BUGS:

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

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