lagan 1.2 biology =0

Efficient tools for large-scale multiple alignments of genomic DNA
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 16 Mar 2006 22:31:50
License: not specified in port

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The LAGAN Toolkit consists of four components: 

 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/

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.
Required To Run: lang/perl5.8
There are no ports dependent upon this port

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To install the port: cd /usr/ports/biology/lagan/ && make install clean
To add the package: pkg_add -r lagan

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Configuration Options

     No options to configure

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Master Sites:

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

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- Get Rid MD5 support

- Unbreak build: CPP is now part of MAKE_ENV

Reported by:    pointyhat

- Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default
MAKE_ENV

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>

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