Package: wnpp Severity: wishlist Owner: Charles Plessy <[EMAIL PROTECTED]>
Package name : ngila Version : 1.2.1 Upstream Author : Reed A. Cartwright <[EMAIL PROTECTED]> or <[EMAIL PROTECTED]> 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 -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
