KALIGN(1)
NAME
kalign - performs multiple alignment of biological sequences.
SYNOPSIS
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
- Gap open penalty .
- -e -gpe -gap_ext -gapextension x
- Gap extension penalty.
- -t -tgpe -terminal_gap_extension_penalty x
- Terminal gap penalties.
- -m -bonus -matrix_bonus x
- A constant added to the substitution matrix.
- -c -sort <input, tree, gaps.>
- The order in which the sequences appear in the output alignment.
- -g -feature
- Selects feature mode and specifies which features are to be used:
e.g. all, maxplp, STRUCT, PFAM-A? - -same_feature_score
- Score for aligning same features.
- -diff_feature_score
- Penalty for aligning different features.
- -d -distance <wu, pair>
- Distance method
- -b -tree -guide-tree <nj, upgma>
- Guide tree method.
- -z -zcutoff
- Parameter used in the wu-manber based distance calculation.
- -i -in -input
- Name of the input file.
- -o -out -output
- Name of the output file.
- -a -gap_inc
- Increases gap penalties depending on the number of existing gaps.
- -f -format <fasta, msf, aln, clu, macsim>
- The output format.
- -q -quiet
- Print nothing to STDERR. Read nothing from STDIN.
REFERENCES
- o Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate
- and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298
- o Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009)
- Kalign2: high-performance multiple alignment of protein and
nucleotide sequences allowing external features. Nucleic Acid
Research 3:858?865.
AUTHORS
- Timo Lassmann <timolassmann@gmail.com>
- Upstream author of Kalign.
- Charles Plessy <plessy@debian.org>
- Wrote the manpage.
COPYRIGHT
Copyright (C) 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 <plessy@debian.org> 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.