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