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1.2
date	2012.11.17.22.22.43;	author svnexp;	state Exp;
branches;
next	1.1;

1.1
date	2006.03.16.22.31.26;	author garga;	state Exp;
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desc
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1.2
log
@## SVN ##
## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/ 307436
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ## r307436 | wen | 2012-11-15 07:04:29 +0000 (Thu, 15 Nov 2012) | 8 lines
## SVN ##
## SVN ## - Update to version 2.0
## SVN ## - Update pkg-descr
## SVN ##
## SVN ## PR:		172497
## SVN ## Submitted by:	KATO Tsuguru <tkato432@@yahoo.com>
## SVN ##
## SVN ## Feature safe:	yes
## SVN ##
## SVN ## ------------------------------------------------------------------------
## SVN ##
@
text
@The Lagan Tookit is a set of alignment programs for comparative
genomics. The three main components are a pairwise aligner (LAGAN), a
multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All
three are based on the CHAOS local alignment tool and combine speed
(regions up to several megabases can be aligned in minutes) with high
accuracy. The results of the alignment can be visualized using the VISTA
visualization tool.

WWW: http://lagan.stanford.edu/
@


1.1
log
@Add lagan 1.2, efficient tools for large-scale multiple alignments of
genomic DNA.

PR:		ports/93058
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar>
@
text
@d1 7
a7 1
The LAGAN Toolkit consists of four components: 
d9 1
a9 22
 CHAOS, a pairwise local aligner optimized for non-coding, and other
 poorly conserved regions of the genome.
 
 LAGAN, a highly parametrizable pairwise global alignment using local
 alignments generated by CHAOS as anchors.
 
 Multi-LAGAN, a progressive pairwise algorithm to produce multiple
 sequence alignments.
 
 Shuffle-LAGAN, a novel glocal algorithm that is able to find
 rearrangements in a global alignment.

Fast and sensitive multiple alignment of long genomic sequences. BMC
Bioinformatics 2003 4:66.

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple
alignment of genomic DNA. Genome Res 2003 13(4): 721-31.

Glocal alignment: finding rearrangements during alignment. Proceedings
of the ISMB 2003, Bioinformatics 19: 54i-62i.

WWW: http://lagan.stanford.edu/lagan_web/
@

