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.TH "alignment\-cat" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-cat\f[] \- Concatenate several alignments (with the same
sequence names) end\-to\-end.
.SH SYNOPSIS
.PP
\f[B]alignment\-cat\f[] \f[I]file1\f[] [\f[I]file2\f[] ...]
.SH DESCRIPTION
.PP
Concatenate several alignments (with the same sequence names)
end\-to\-end.
.SH ALL OPTIONS:
.TP
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
Produce help message
.RS
.RE
.TP
.B \f[B]\-\-output\f[] \f[I]arg\f[] (=fasta)
Which output format: fasta or phylip?
.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]\-t\f[] \f[I]arg\f[], \f[B]\-\-taxa\f[] \f[I]arg\f[]
Taxa to keep, comma\-separated
.RS
.RE
.TP
.B \f[B]\-p\f[], \f[B]\-\-pad\f[]
Add gaps to make sequence lengths identical
.RS
.RE
.TP
.B \f[B]\-r\f[], \f[B]\-\-reverse\f[]
Reverse the sequences
.RS
.RE
.TP
.B \f[B]\-e\f[], \f[B]\-\-erase\-empty\-columns\f[]
Remove columns with no characters (all gaps).
.RS
.RE
.TP
.B \f[B]\-\-missing\f[] \f[I]arg\f[] (=\-?)
What letters are not characters (e.g.
gaps)?
.RS
.RE
.TP
.B \f[B]\-\-strip\-gaps\f[]
Remove all non\-character letters from sequences.
.RS
.RE
.TP
.B \f[B]\-\-reorder\-by\-tree\f[] \f[I]arg\f[]
Reorder the sequences given a tree
.RS
.RE
.TP
.B \f[B]\-\-use\-root\f[]
use the root specified in the tree file to reorder
.RS
.RE
.TP
.B \f[B]\-\-reorder\-by\-alignment\f[] \f[I]arg\f[]
Reorder the sequences following an alignment
.RS
.RE
.TP
.B \f[B]\-\-align\-by\-amino\f[] \f[I]arg\f[]
Arrange nucleotides into codon alignment
.RS
.RE
.SH EXAMPLES:
.PP
To select columns from an alignment:
.IP
.nf
\f[C]
%\ alignment\-cat\ \-c1\-10,50\-100,600\-\ filename.fasta\ >\ result.fasta
%\ alignment\-cat\ \-c5\-250/3\ filename.fasta\ >\ first_codon_position.fasta
%\ alignment\-cat\ \-c6\-250/3\ filename.fasta\ >\ second_codon_position.fasta
\f[]
.fi
.PP
To concatenate two or more alignments:
.IP
.nf
\f[C]
%\ alignment\-cat\ filename1.fasta\ filename2.fasta\ >\ all.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.