MMseqs2: ultra fast and sensitive search and clustering suite

Remote protein homology detection suite.

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Direct IO helpers for block devices and regular files on FreeBSD, Linux, macOS and Windows.

parallelized blat with multi-threads support

Memory Manager - Fast, Scalable and Easy to use

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.

Dynamic memory pool implementation, for reusable fixed, or variable sized memory blocks, using pthread mutex locks.

Long-read aligner to pangenome graphs

C library to print nicely formatted tables

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

Short implementation (~500 lines) of the Gotoh algorithm, a.k.a. Needleman-Wunsch with affine gap penalties.

An extension to the wavefront algorithm that generalizes it to work on directed acyclic sequence graphs

A SNP-aware short read aligner

blat with cluster parallel hybrid computing support

Generalized edit distance command line tool

Fast heuristic methods of detecting adaptive evolution in protein-coding genes.

Reference-based alignment and sequence database search of SARS-CoV-2 genomes.