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.TH "alignment-cat" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment-cat\f[R] - Concatenate several alignments (with the same
sequence names) end-to-end.
.SH SYNOPSIS
.PP
\f[B]alignment-cat\f[R] \f[I]file1\f[R] [\f[I]file2\f[R] ...]
.SH DESCRIPTION
.PP
Concatenate several alignments (with the same sequence names)
end-to-end.
.SH ALL OPTIONS:
.TP
\f[B]-h\f[R], \f[B]--help\f[R]
Produce help message
.TP
\f[B]--output\f[R] \f[I]arg\f[R] (=fasta)
Which output format: fasta or phylip?
.TP
\f[B]-c\f[R] \f[I]arg\f[R], \f[B]--columns\f[R] \f[I]arg\f[R]
Ranges of columns to keep, like: 1-10,30-
.TP
\f[B]-t\f[R] \f[I]arg\f[R], \f[B]--taxa\f[R] \f[I]arg\f[R]
Taxa to keep, comma-separated
.TP
\f[B]-p\f[R], \f[B]--pad\f[R]
Add gaps to make sequence lengths identical
.TP
\f[B]-r\f[R], \f[B]--reverse\f[R]
Reverse the sequences
.TP
\f[B]-e\f[R], \f[B]--erase-empty-columns\f[R]
Remove columns with no characters (all gaps).
.TP
\f[B]--missing\f[R] \f[I]arg\f[R] (=-?)
What letters are not characters (e.g.
gaps)?
.TP
\f[B]--strip-gaps\f[R]
Remove all non-character letters from sequences.
.TP
\f[B]--reorder-by-tree\f[R] \f[I]arg\f[R]
Reorder the sequences given a tree
.TP
\f[B]--use-root\f[R]
use the root specified in the tree file to reorder
.TP
\f[B]--reorder-by-alignment\f[R] \f[I]arg\f[R]
Reorder the sequences following an alignment
.TP
\f[B]--align-by-amino\f[R] \f[I]arg\f[R]
Arrange nucleotides into codon alignment
.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[R]
.fi
.PP
To concatenate two or more alignments:
.IP
.nf
\f[C]
% alignment-cat filename1.fasta filename2.fasta > all.fasta
\f[R]
.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.