sequence-alignment

There are 18 repositories under sequence-alignment topic.

biopython / biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Language:Python 4165
lh3 / minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics genomics sequence-alignment spliced-alignment
Language:C 1684
lh3 / bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics fm-index genomics sequence-alignment
Language:C 1451
bbuchfink / diamond
Accelerated BLAST compatible local sequence aligner.
sequence-alignment
Language:C++ 954
bwa-mem2 / bwa-mem2
The next version of bwa-mem
bioinformatics genomics sequence-alignment
Language:C++ 675
torognes / vsearch
Versatile open-source tool for microbiome analysis
metabarcoding metagenomics chimera bioinformatics fastq fasta microbiome amplicon sequence-alignment clustering search
Language:C++ 627
biojava / biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
bioinformatics java protein-structure genomics protein-sequences protein-modification sequence-alignment structure-alignment protein-data-bank pdb parser-library structural-bioinformatics
Language:Java 575
Martinsos / edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
sequence-alignment edit-distance levehnstein-distance library c-plus-plus alignment-path python bioinformatics
Language:C++ 485
seqan3
seqan / seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
sequence-analysis seqan cpp17 cpp20 cpp-concepts bioinformatics blast sequence-alignment fasta fastq samtools fm-index modern
Language:C++ 388
lh3 / minigraph
Sequence-to-graph mapper and graph generator
bioinformatics genome-graph genomics pan-genome sequence-alignment
Language:C 387
microsoft / bistring
Bidirectionally transformed strings
string sequence-alignment
Language:Python 367
lh3 / miniprot
Align proteins to genomes with splicing and frameshift
bioinformatics sequence-alignment
Language:C 296
wurmlab / sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
blast bioinformatics sequencing genomics-visualization genomics visualization sequence-alignment hacktoberfest ruby javascript
Language:JavaScript 265
lh3 / ksw2
Global alignment and alignment extension
bioinformatics sequence-alignment
Language:C 123
TimoLassmann / kalign
A fast multiple sequence alignment program.
sequence-alignment bioinformatics sequence-analysis
Language:C 115
flatironinstitute / deepblast
Neural Networks for Protein Sequence Alignment
structural-alignments neural-networks sequence-alignment language-modeling protein-sequences protein protein-structure
Language:Python 96
cogent3 / cogent3
Comparative Genomics Toolkit 3
bioinformatics pycogent statistics data-science biology genomics evolution biopython markov-chain molecular-evolution non-stationary phylogenetic-trees phylogenetics python parallel signal-processing maximum-likelihood biological-sequence-analysis sequence-alignment
Language:Python 93
lh3 / unimap
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
bioinformatics genomics sequence-alignment
Language:C 84
MicrobeTrace
CDCgov / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics epidemiology network-visualization hiv cdc pathogens phylogenetics phylogenetic-trees phylogeny phylogenomics genomics genomics-visualization genomic-data-analysis sequence-alignment
Language:TypeScript 83
drostlab / orthologr
Genome wide orthology inference and dNdS estimation
blast-searches orthology-inference comparative-genomics-studies genomics sequence-alignments blast comparative dnds-estimation codon-alignment r entire-genomes orthologous-genes biomartr species comparing-genomes genomics-studies retrieve-genomes comparative-genomics proteome sequence-alignment
Language:R 82
pyMSAviz
moshi4 / pyMSAviz
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
bioinformatics matplotlib msa python sequence-analysis visualization genomics multiple-sequence-alignment sequence-alignment
Language:Python 65
zhou-lab / biscuit
BISulfite-seq CUI Toolkit
dna-methylation sequence-alignment bioinformatics
Language:C 62
biocommons / uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
bioinformatics sequence-alignment sequences
Language:Python 60
BioJulia / BioAlignments.jl
Sequence alignment tools
bam-files sam-files sequence-alignment sequence-analysis dna-sequences biology bioinformatics smith-waterman-alignment high-throughput-sequencing biojulia
Language:Julia 58
kensho-technologies / sequence_align
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
hirschberg needleman-wunsch pyo3 python rust sequence-alignment bioinformatics natural-language-processing nlp
Language:Python 57
RWilton / Arioc
Arioc: GPU-accelerated DNA short-read alignment
bioinformatics genomics read-aligners sequence-alignment dna-sequence-alignment gpu bisulfite-sequencing methylation cuda c-plusplus variant-analysis
54
jguhlin / minimap2-rs
Rust bindings to minimap2 library
alignment bioinformatics ffi longread minimap2 rust genomics sequence-alignment spliced-alignment
Language:Rust 51
rdpstaff / RDPTools
Collection of commonly used RDP Tools for easy building
16s bioinformatics microbiome microbiology bayesian-classifiers sequence-alignment
Language:Makefile 49
lh3 / miniwfa
A reimplementation of the WaveFront Alignment algorithm at low memory
bioinformatics sequence-alignment
Language:C 48
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.
sequence-aligner fpga gpu hardware-accelerator minimap2 edlib smith-waterman needleman-wunsch pre-alignment-filtering sequence-alignment long-reads short-reads wavefront-alignment
Language:VHDL 46
ITBE-Lab / MA
The Modular Aligner and The Modular SV Caller
alignment bioinformatics sequence-alignment read-aligners fm-index structural-variation seeds
Language:C++ 45
estebanpw / chromeister
A dotplot generator for large chromosomes
dotplot chromosomes genome genome-comparisons genomics sequence-alignment plants fast lightweight
Language:C 39
nahmedraja / GASAL2
sequence-alignment gpu-acceleration cuda-library bioinfomatics
Language:C++ 39
lh3 / bioseq-js
For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml
bioinformatics sequence-alignment
Language:HTML 37
Martinsos / opal
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
sequence-alignment bioinformatics smith-waterman c-plus-plus avx alignment database-search
Language:C++ 34
arshajii / ema
Fast & accurate alignment of barcoded short-reads
bioinformatics sequence-alignment
Language:C++ 32