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% alignments-diff(1)
% Benjamin Redelings
% Feb 2018
# 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>.
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