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.TH "alignment\-indices" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-indices\f[] \- Show the alignment in terms of the index
of each character in its sequence.
.SH SYNOPSIS
.PP
\f[B]alignment\-indices\f[] \f[I]alignment\-file\f[] [OPTIONS]
.SH DESCRIPTION
.PP
Show the alignment in terms of the index of each character in its
sequence.
.SH ALLOWED OPTIONS:
.TP
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
produce help message
.RS
.RE
.TP
.B \f[B]\-\-align\f[] \f[I]arg\f[]
file with sequences and initial alignment
.RS
.RE
.TP
.B \f[B]\-\-alphabet\f[] \f[I]arg\f[]
set to \[aq]Codons\[aq] to prefer codon alphabets
.RS
.RE
.TP
.B \f[B]\-c\f[] \f[I]arg\f[], \f[B]\-\-columns\f[] \f[I]arg\f[]
Ranges of columns to keep, like: 1\-10,30\-
.RS
.RE
.TP
.B \f[B]\-\-invariant\f[] \f[I]arg\f[]
print only sites where this site and neighbors are invariant.
.RS
.RE
.TP
.B \f[B]\-\-differences\f[] \f[I]arg\f[]
how many sequences may differ from the majority?
.RS
.RE
.TP
.B \f[B]\-\-avoid\-gaps\f[] \f[I]arg\f[] (=3)
How far from a gap must a column be to be invariant?
.RS
.RE
.TP
.B \f[B]\-\-min\-constraints\f[] \f[I]arg\f[]
Minimum # of constraints per column for a constraint to be emitted
.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.