Package: wnpp Severity: wishlist Subject: ITP: libwfa2 -- exact gap-affine algorithm Package: wnpp Owner: Andreas Tille <ti...@debian.org> Severity: wishlist
* Package name : libwfa2 Version : 2.3.1 Upstream Author : Santiago Marco-Sola <santiagoms...@gmail.com> * URL : https://github.com/smarco/WFA2-lib * License : MIT Programming Lang: C Description : exact gap-affine algorithm The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. Unlike to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns+s^2), proportional to the sequence length n and the alignment score s, using O(s^2) memory (or O(s) using the ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple computational patterns that the modern compilers can automatically vectorize for different architectures without adapting the code. To intuitively illustrate why the WFA algorithm is so interesting, look at the following figure. The left panel shows the cells computed by a classical dynamic programming based algorithm (like Smith-Waterman or Needleman Wunsch). In contrast, the right panel shows the cells computed by the WFA algorithm to obtain the same result (i.e., the optimal alignment). Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/libwfa2
