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.TH "alignment-chop-internal" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment-chop-internal\f[R] - Remove ancestral sequences from an
alignment.
.SH SYNOPSIS
.PP
\f[B]alignment-chop-internal\f[R] [OPTIONS] < \f[I]alignments-file\f[R]
.SH DESCRIPTION
.PP
Remove ancestral sequences from an alignment.
.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]\[en]tree\f[R] \f[I]arg\f[R]
file with tree that specifies leaves to keep
.TP
\f[B]-N\f[R] \f[I]arg\f[R], \f[B]\[en]nleaves\f[R] \f[I]arg\f[R]
number of sequences to keep
.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.