.\" Automatically generated by Pandoc 2.2.1
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.TH "alignment\-thin" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-thin\f[] \- Remove sequences or columns from an
alignment.
.SH SYNOPSIS
.PP
\f[B]alignment\-thin\f[] \f[I]alignment\-file\f[] [OPTIONS]
.SH DESCRIPTION
.PP
Remove sequences or columns from an alignment.
.SH GENERAL OPTIONS:
.TP
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
Print usage information.
.RS
.RE
.TP
.B \f[B]\-v\f[], \f[B]\-\-verbose\f[]
Output more log messages on stderr.
.RS
.RE
.SH SEQUENCE FILTERING OPTIONS:
.TP
.B \f[B]\-\-protect\f[] \f[I]arg\f[]
Sequences that cannot be removed (comma\-separated).
.RS
.RE
.TP
.B \f[B]\-\-remove\f[] \f[I]arg\f[]
Remove sequences in comma\-separated list \f[I]arg\f[].
.RS
.RE
.TP
.B \f[B]\-\-longer\-than\f[] \f[I]arg\f[]
Remove sequences not longer than \f[I]arg\f[].
.RS
.RE
.TP
.B \f[B]\-\-shorter\-than\f[] \f[I]arg\f[]
Remove sequences not shorter than \f[I]arg\f[].
.RS
.RE
.TP
.B \f[B]\-\-cutoff\f[] \f[I]arg\f[]
Remove similar sequences with #mismatches < cutoff.
.RS
.RE
.TP
.B \f[B]\-\-down\-to\f[] \f[I]arg\f[]
Remove similar sequences down to \f[I]arg\f[] sequences.
.RS
.RE
.TP
.B \f[B]\-\-remove\-crazy\f[] \f[I]arg\f[]
Remove \f[I]arg\f[] outlier sequences \-\- defined as sequences that are
missing too many conserved sites.
.RS
.RE
.TP
.B \f[B]\-\-conserved\f[] \f[I]arg\f[] (=0.75)
Fraction of sequences that must contain a letter for it to be considered
conserved.
.RS
.RE
.SH COLUMN FILTERING OPTIONS:
.TP
.B \f[B]\-\-min\-letters\f[] \f[I]arg\f[]
Remove columns with fewer than \f[I]arg\f[] letters.
.RS
.RE
.TP
.B \f[B]\-\-remove\-unique\f[] \f[I]arg\f[]
Remove insertions in a single sequence if longer than \f[I]arg\f[]
letters
.RS
.RE
.SH OUTPUT OPTIONS:
.TP
.B \f[B]\-\-sort\f[]
Sort partially ordered columns to group similar gaps.
.RS
.RE
.TP
.B \f[B]\-\-show\-lengths\f[]
Just print out sequence lengths.
.RS
.RE
.TP
.B \f[B]\-\-find\-dups\f[] \f[I]arg\f[]
For each sequence, find the closest other sequence.
.RS
.RE
.SH EXAMPLES:
.PP
Remove columns without a minimum number of letters:
.IP
.nf
\f[C]
%\ alignment\-thin\ \-\-min\-letters=5\ file.fasta\ >\ file\-thinned.fasta
\f[]
.fi
.PP
Remove sequences by name:
.IP
.nf
\f[C]
%\ alignment\-thin\ \-\-remove=seq1,seq2\ file.fasta\ >\ file2.fasta
\f[]
.fi
.PP
Remove short sequences:
.IP
.nf
\f[C]
%\ alignment\-thin\ \-\-longer\-than=250\ file.fasta\ >\ file\-long.fasta
\f[]
.fi
.PP
Remove sequences with <= 5 differences from the closest other sequence:
.IP
.nf
\f[C]
%\ alignment\-thin\ \-\-cutoff=5\ file.fasta\ >\ more\-than\-5\-differences.fasta
\f[]
.fi
.PP
Like \-\-cutoff, but stop when we have the right number of sequences:
.IP
.nf
\f[C]
%\ alignment\-thin\ \-\-down\-to=30\ file.fasta\ >\ file\-30taxa.fasta
\f[]
.fi
.PP
Remove dissimilar sequences that are missing conserved columns:
.IP
.nf
\f[C]
%\ alignment\-thin\ \-\-remove\-crazy=10\ file.fasta\ >\ file2.fasta
\f[]
.fi
.PP
Protect some sequences from being removed:
.IP
.nf
\f[C]
%\ alignment\-thin\ \-\-down\-to=30\ file.fasta\ \-\-protect=seq1,seq2\ >\ file2.fasta
\f[]
.fi
.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.