.\" Automatically generated by Pandoc 2.2.1
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.TH "alignments\-diff" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignments\-diff\f[] \- Align two alignments for comparison.
.SH SYNOPSIS
.PP
\f[B]alignments\-diff\f[] alignment\-file1 alignment\-file2 [OPTIONS]
.SH DESCRIPTION
.PP
Align two alignments for comparison.
.SH GENERAL OPTIONS:
.TP
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
produce help message
.RS
.RE
.SH INPUT OPTIONS:
.TP
.B \f[B]\-\-alphabet\f[] \f[I]arg\f[]
set to \[aq]Codons\[aq] to prefer codon alphabets
.RS
.RE
.SH OUTPUT OPTIONS:
.TP
.B \f[B]\-\-merge\f[]
Stack the two alignments into one alignment with duplicate names
.RS
.RE
.TP
.B \f[B]\-\-dual\f[]
Write out the two aligned alignments separately
.RS
.RE
.TP
.B \f[B]\-\-fill\f[] \f[I]arg\f[] (=gap)
blank columns filled with: gap or unknown
.RS
.RE
.TP
.B \f[B]\-d\f[] \f[I]arg\f[], \f[B]\-\-differences\-file\f[] \f[I]arg\f[]
Filename to store differences in AU format
.RS
.RE
.SH REPORTING BUGS:
.PP
BAli\-Phy online help: <http://www.bali-phy.org/docs.php>.
.PP
Please send bug reports to <bali-phy-users@googlegroups.com>.
.SH AUTHORS
Benjamin Redelings.