debian man page for kalign

Query: kalign

OS: debian

Section: 1

Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

KALIGN(1)							Kalign User Manual							 KALIGN(1)

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
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)
Related Man Pages
cdhit-est-2d(1) - debian
proda(1) - debian
sigma(1) - debian
ssematch(1e) - debian
bio::tools::run::alignment::kalign(3pm) - debian
Similar Topics in the Unix Linux Community
parsing data and incorporating it into another file
Editing headers
editing headers
Is it possible to rename fasta headers based on its position specified in another file?
How to find a specific sequence pattern in a fasta file?