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sigma-align

Simple greedy multiple alignment of non-coding DNA sequences

Variants:
Sigma (“Simple greedy multiple alignment”) is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. It uses a strategy of seeking the best possible gapless local alignments, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA.
Homepage:
Package version:1.1.3-1
Architecture:i386
Distribution:Debian
Filename:sigma-align_1.1.3-1_i386.deb

/usr/share/doc/sigma-align/README

Sigma: Simple greedy multiple alignment
Version 1.1.3, (C) 2009, Rahul Siddharthan <rsidd@imsc.res.in>
Portions written and (C) 2009, Gayathri Jayaraman

This is a port to C of Sigma, which was originally (version 1.0)
written in ocaml.  A paper describing the algorithm was published in
BMC Bioinformatics 7:143 (2006).  A couple of important bugs have
been fixed, and it is about 3 to 4 times faste
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/usr/share/doc/sigma-align/NEWS.gz

Version 1.1 released April 3, 2007: rewrite in C

/usr/share/man/man1/sigma.1.gz

SIGMA(1)                   Manual of Sigma                  SIGMA(1)



NAME
       sigma - Simple greedy multiple alignment of non-coding DNA
       sequences

SYNOPSIS
       sigma [options] [inputfile.fasta] [inputfile2.fasta ...]

       Each fasta file may contain a single sequence or multiple
       sequences; all sequences will be aligned together.

DESCRIPTION
       Sigma ("Simple greedy 
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/usr/share/doc/sigma-align/changelog.Debian.gz

sigma-align (1.1.3-1) unstable; urgency=low

  * New upstream release.
  * Converted the packaging t
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/usr/share/doc/sigma-align/changelog.gz

Version 1.1.3:
  * Make local gapless alignment function linear in memory consumption
    (Gayathri 
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/usr/share/doc/sigma-align/AUTHORS

Rahul Siddharthan <rsidd@imsc.res.in> 
The Institute of Mathematical Sciences, Chennai 600 113, Indi
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/usr/share/doc/sigma-align/copyright

Name: Sigma
Source: http://www.imsc.res.in/~rsidd/sigma/source/sigma-1.1.3.tar.gz
Contact: Rahul Sid
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