kalign(1) 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]



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.


-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?


Score for aligning same features.


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.


•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.


Timo Lassmann <[email protected]>

Upstream author of Kalign.

Charles Plessy <[email protected]>

Wrote the manpage.


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 protected]> 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.