MMseqs2: ultra fast and sensitive search and clustering suite
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Updated
Jun 11, 2024 - C
MMseqs2: ultra fast and sensitive search and clustering suite
Remote protein homology detection suite.
Direct IO helpers for block devices and regular files on FreeBSD, Linux, macOS and Windows.
parallelized blat with multi-threads support
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.
Memory Manager - Fast, Scalable and Easy to use
PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT
Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria
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
blat with cluster parallel hybrid computing support
Generalized edit distance command line tool
Reference-based alignment and sequence database search of SARS-CoV-2 genomes.
Fast heuristic methods of detecting adaptive evolution in protein-coding genes.
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