sequence-alignment

lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

lh3/bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

bbuchfink/diamond

Accelerated BLAST compatible local sequence aligner.

bwa-mem2/bwa-mem2

The next version of bwa-mem

torognes/vsearch

Versatile open-source tool for microbiome analysis

biojava/biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Martinsos/edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

lh3/minigraph

Sequence-to-graph mapper and graph generator

seqan/seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

lh3/miniprot

Align proteins to genomes with splicing and frameshift

microsoft/bistring

Bidirectionally transformed strings

wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

shenwei356/LexicMap

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

moshi4/pyMSAviz

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

TimoLassmann/kalign

A fast multiple sequence alignment program.

lh3/ksw2

Global alignment and alignment extension

cogent3/cogent3

Comparative Genomics Toolkit 3

flatironinstitute/deepblast

Neural Networks for Protein Sequence Alignment

jguhlin/minimap2-rs

Rust bindings to minimap2 library

drostlab/orthologr

Genome wide orthology inference and dNdS estimation

CDCgov/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

lh3/unimap

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

kensho-technologies/sequence_align

Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

biocommons/uta

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

RWilton/Arioc

Arioc: GPU-accelerated DNA short-read alignment

zhou-lab/biscuit

BISulfite-seq CUI Toolkit

BioJulia/BioAlignments.jl

Sequence alignment tools

CMU-SAFARI/SneakySnake

SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.

rdpstaff/RDPTools

Collection of commonly used RDP Tools for easy building

lh3/miniwfa

A reimplementation of the WaveFront Alignment algorithm at low memory

nahmedraja/GASAL2

ITBE-Lab/MA

The Modular Aligner and The Modular SV Caller

estebanpw/chromeister

A dotplot generator for large chromosomes

lh3/bioseq-js

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

Martinsos/opal

SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)