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kalign - Online in the Cloud

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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

PROGRAM:

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


· 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.

AUTHORS


Timo Lassmann <[email protected]>
Upstream author of Kalign.

Charles Plessy <[email protected]>
Wrote the manpage.

COPYRIGHT


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 <[email protected]> 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.

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