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       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]


       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.


       -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

       ·   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 <>
           Upstream author of Kalign.

       Charles Plessy <>
           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 <> 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.