KALIGN(1)							Kalign User Manual							 KALIGN(1)

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. kalign 2.04 February 25, 2009 KALIGN(1)

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