sequence-alignment
There are 328 repositories under sequence-alignment topic.
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
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.
seqan/seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
lh3/minigraph
Sequence-to-graph mapper and graph generator
microsoft/bistring
Bidirectionally transformed strings
lh3/miniprot
Align proteins to genomes with splicing and frameshift
wurmlab/sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
lh3/ksw2
Global alignment and alignment extension
TimoLassmann/kalign
A fast multiple sequence alignment program.
flatironinstitute/deepblast
Neural Networks for Protein Sequence Alignment
cogent3/cogent3
Comparative Genomics Toolkit 3
shenwei356/LexicMap
LexicMap: efficient sequence alignment against millions of prokaryotic genomes
CDCgov/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
drostlab/orthologr
Genome wide orthology inference and dNdS estimation
lh3/unimap
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
moshi4/pyMSAviz
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
kensho-technologies/sequence_align
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
zhou-lab/biscuit
BISulfite-seq CUI Toolkit
biocommons/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
BioJulia/BioAlignments.jl
Sequence alignment tools
jguhlin/minimap2-rs
Rust bindings to minimap2 library
RWilton/Arioc
Arioc: GPU-accelerated DNA short-read alignment
lh3/miniwfa
A reimplementation of the WaveFront Alignment algorithm at low memory
rdpstaff/RDPTools
Collection of commonly used RDP Tools for easy building
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.
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)