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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 <> Upstream author of Kalign. Charles Plessy <> 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 <> 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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GLAM2FORMAT(1)							   glam2 Manual 						    GLAM2FORMAT(1)

glam2format - converts GLAM2 motifs to FASTA or MSF format SYNOPSIS
glam2format [options] my_format my_motif.glam2 Formats: fasta, msf. DESCRIPTION
glam2format reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in glam2 output is converted. OPTIONS (DEFAULT SETTINGS) -o Output file (stdout). -c Make a compact alignment. By default, residues that are inserted between key positions are written as unaligned with each other. This best reflects glam2's intention, but it can make the alignment large and full of gaps. With -c, inserted residues are written as arbitrarily aligned with each other, just as they appear in the glam2 output. -f Sequence file to make a "global" alignment by adding flanking sequences from the original FASTA-format sequence file. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the -c option. The sequences should have unique names and their order should be unchanged. SEE ALSO
boxshade(1), glam2(1), glam2mask(1), glam2-purge(1), glam2scan(1) The full Hypertext documentation of GLAM2 is available online at or on this computer in /usr/share/doc/glam2/. REFERENCE
If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). AUTHORS
Martin Frith Author of GLAM2. Timothy Bailey Author of GLAM2. Charles Plessy <> Formatted this manpage in DocBook XML for the Debian distribution. COPYRIGHT
The source code and the documentation of GLAM2 are released in the public domain. GLAM2 1056 05/19/2008 GLAM2FORMAT(1)
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