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