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
· Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate
and fast multiple sequence alignment algorithm. BMC Bioinformatics
6:298
· 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 © 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.