|KALIGN(1)||Kalign User Manual||KALIGN(1)|
NAME¶kalign - performs multiple alignment of biological sequences.
kalign [infile.fasta] [outfile.fasta] [Options]
kalign [-i infile.fasta] [-o outfile.fasta] [Options]
kalign [< infile.fasta] [> outfile.fasta] [Options]
DESCRIPTION¶Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm, to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment.
OPTIONS¶-s -gpo -gapopen -gap_open x
-e -gpe -gap_ext -gapextension x
-t -tgpe -terminal_gap_extension_penalty x
-m -bonus -matrix_bonus x
-c -sort <input, tree, gaps.>
-d -distance <wu, pair>
-b -tree -guide-tree <nj, upgma>
-i -in -input
-o -out -output
-f -format <fasta, msf, aln, clu, macsim>
AUTHORS¶Timo Lassmann <email@example.com>
- Upstream author of Kalign.
Charles Plessy <firstname.lastname@example.org>
- Wrote the manpage.
COPYRIGHT¶Copyright © 2004, 2005, 2006, 2007, 2008 Timo Lassmann
Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.
This manual page was written by Charles Plessy <email@example.com> for the Debian(TM) system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as kalign itself.
On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common-licenses/GPL-2.
|February 25, 2009||kalign 2.04|