Application of two different algorithms for sequence alignment

AlnSeq runs a c coded Smith Waterman, Needleman Wunsch, and an Hirschberg. It can run as a standalone or as a library for python.

This is a fork of PROMALS3D

ALPHAMALIG(ALPHAbet Multiple ALIGnment)

A fast multiple sequence alignment program.

Parallel sequence alignment program that finds the optimal mutation in one sequence of the other. Parallelizes CPU and GPU using OpenMP and CUDA, and communicates with multiple computers using MPI.

🧬 Implementation of the Smith-Waterman algorithm for aligning amino acid sequences.

🧬🔍 Smith-Waterman pairwise sequences alignment ✍️🔡

A parallelized version of multiple DNA sequence alignment algorithm with MPI, OpenMP and CUDA

bvSFM (bit-vector sampled FM-index) is a tool for sequence alignment.

Illumina (and SOLiD) sensitive read mapping tool (cloned from svn://scm.gforge.inria.fr/svnroot/storm/)

A CUDA library of DNA/RNA sequence alignment algorithms.

GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.

Fast implementation of Ukkenon's O(ND) algorithm for computing edit distance

GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Described in the ASPLOS 2022 paper by Mansouri Ghiasi et al. at https://people.inf.ethz.ch/omutlu/pub/GenS…

Short reads aligner for NIPT/CNV

genomic alignment similarity search tool

AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.org/10.1093/bioinformatics/btad155

GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment

A dotplot generator for large chromosomes