Racon
Racon is the state-of-the-art tool for the consensus and/or polishing of genome assemblies. SPOA its core module is a SIMD accelerated multiple sequence alignment tool
Raven
Raven is a straightforward, fast, and memory-efficient de novo assembler optimized for work with Nanopore and Pacbio CLR sequenced data.
Edlib
Edlib is a lightweight, super-fast library for sequence alignment using edit (Levenshtein) distance.
Graphmap
Graphmap/Graphmap2 is a fast and sensitive tool for the alignment of DNA or RNA long reads to the reference genome.
PSAIA
PSAIA is a popular command line, and GUI based tool for fast calculation of various protein structure features such as solvent-accessible surface and interaction sites.
SW#
SW# is a GPU accelerated tool for the calculation of the exact alignment of long sequences.
Spoa
Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences.