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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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