J. Daily, "Parasail: SIMD c library for global, semi-global, and local pairwise sequence alignments," BMC Bioinformatics, vol. 17, no. 1, feb 2016. [Online]. Available: https://doi.org/10.1186/s12859-016-0930-zDaily, J. (2016). Parasail: SIMD C library for global, semi-global, ...
Opal (ex Swimd) is SIMD C/C++ library for massive optimal sequence alignment. Opal is implemented mainly by Rognes's "Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation". Main difference is that Opal offers support for AVX2 and 4 alignment modes instead of just ...
abPOA is not only a stand-alone tool for MSA and consensus calling, it can also work as a library. example.c shows how to use the C APIs of abPOA to take a set of sequences as input and perform MSA and consensus calling, and abPOA_example.vcxproj shows how to use the libraries....
SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications Ssw library: An simd smith-waterman c/c++ library for use in genomic applications. PLoS ONE. 2013;8(12):82138. doi:10.1371/journal.pone.0082138.M. Zhao et al.: SSW Library: an SIMD Smith-Waterman C/C++...
library is shown in Figure 1. This example can be compiled to generate LLVM Vector IR and binary for coreavx512. namespacestdsimd=std::experimental;voidsimd_memcpy(stdsimd::native_simd<float>x,stdsimd::native_simd<float>y,void*p){autocmp=x<y;memcpy(p,&cmp,cmp.size()*4);} ...
Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruct... SM Bhandarkar,S Chirravuri,J Arnold - 《Journal of Computational Biology A Journal of Computational Molecular Cell Biology》 被引量: 13发表: ...
This is the vector classes (Vc) library [4]. It supports all types of CPU's instructions, and also the GPU's LRBni instructions set. Thus, Vc usage expands development possibilities for benchmark. In order to implement vector classes into the SIMD KF fit benchmark some types and ...
This section describes the C/C++ language-level features supporting the Streaming SIMD Extensions 2 (SSE2) instructions:Floating-Point Intrinsics Using Streaming SIMD Extensions 2 Instructions that describe the intrinsic operations for the double-precision, floating-point data type (__m128d). Integer ...
A Skeleton Library for Cell Broadband Engine simd optimizationskeleton programmingCell Broadband Engine is a heterogeneous multicore processor for high-performance computing and gaming. Its architecture allows... M Ålind - PELAB, Dept. of Computer and Information Science Linkoeping university, S-581...
SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications Background The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fas... M Zhao,WP Lee,EP Garrison,... - 《Plos One》 被...