.\" Automatically generated by Pandoc 3.0.1
.\"
.\" Define V font for inline verbatim, using C font in formats
.\" that render this, and otherwise B font.
.ie "\f[CB]x\f[]"x" \{\
. ftr V B
. ftr VI BI
. ftr VB B
. ftr VBI BI
.\}
.el \{\
. ftr V CR
. ftr VI CI
. ftr VB CB
. ftr VBI CBI
.\}
.TH "alignments-diff" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignments-diff\f[R] - Align two alignments for comparison.
.SH SYNOPSIS
.PP
\f[B]alignments-diff\f[R] alignment-file1 alignment-file2 [OPTIONS]
.SH DESCRIPTION
.PP
Align two alignments for comparison.
.SH GENERAL OPTIONS:
.TP
\f[B]-h\f[R], \f[B]\[en]help\f[R]
produce help message
.SH INPUT OPTIONS:
.TP
\f[B]\[en]alphabet\f[R] \f[I]arg\f[R]
set to `Codons' to prefer codon alphabets
.SH OUTPUT OPTIONS:
.TP
\f[B]\[en]merge\f[R]
Stack the two alignments into one alignment with duplicate names
.TP
\f[B]\[en]dual\f[R]
Write out the two aligned alignments separately
.TP
\f[B]\[en]fill\f[R] \f[I]arg\f[R] (=gap)
blank columns filled with: gap or unknown
.TP
\f[B]-d\f[R] \f[I]arg\f[R], \f[B]\[en]differences-file\f[R] \f[I]arg\f[R]
Filename to store differences in AU format
.TP
\f[B]\[en]blocksize\f[R] \f[I]arg\f[R] (=20)
Width of blocks of same color
.TP
\f[B]\[en]classes\f[R] \f[I]arg\f[R] (=1)
Number of groups for non-matching characters
.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.