Bug#439996: ITP: ngila -- global pairwise alignments with logarithmic and affine gap costs
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>
Package name : ngila
Version : 1.2.1
Upstream Author : Reed A. Cartwright <reed@scit.us> or <racartwr@ncsu.edu>
URL : http://scit.us/projects/ngila/
License : GPL v3 or later
Programming Lang: C++
Description : global pairwise alignments with logarithmic and affine gap costs
Ngila is an application that will find the best alignment of a pair
of sequences using log-affine gap costs, which are the most
biologically realistic gap costs.
.
Ngila implements the Miller and Myers (1988) algorithm in order to
find a least costly global alignment of two sequences given homology
costs and a gap cost. Two versions of the algorithm are
included: holistic and divide-and-conquer. The former is faster but
the latter utilizes less memory. Ngila starts with the
divide-and-conquer method but switches to the holistic method for
subsequences smaller than a user-established threshold. This improves
its speed without substantially increasing memory requirements. Ngila
also allows users to assign costs to end gaps that are smaller than
costs for internal gaps. This is important for aligning using the
free-end-gap method.
.
Ngila is published in Cartwright RA Bioinformatics 2007
23(11):1427-1428; doi:10.1093/bioinformatics/btm095
.
Homepage: http://scit.us/projects/ngila/
--
Charles Plessy
Debian-Med packaging team
Wako, Saitama, Japan
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