table of contents
| 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 xGap 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 <timolassmann@gmail.com>- Upstream author of Kalign.
- Wrote the manpage.
COPYRIGHT¶
Copyright © 2004, 2005, 2006, 2007, 2008 Timo Lassmann| February 25, 2009 | kalign 2.04 |