This is the command kalign that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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.
Selects feature mode and specifies which features are to be used: e.g. all, maxplp,
Score for aligning same features.
Penalty for aligning different features.
-d -distance <wu, pair>
-b -tree -guide-tree <nj, upgma>
Guide tree method.
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.
Increases gap penalties depending on the number of existing gaps.
-f -format <fasta, msf, aln, clu, macsim>
The output format.
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 <firstname.lastname@example.org>
Upstream author of Kalign.
Charles Plessy <email@example.com>
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 <firstname.lastname@example.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.
Use kalign online using onworks.net services