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biopython biopython

1.7k

4.2k

other

168

Official git repository for Biopython (originally converted from CVS)

dna python protein genomics biopython phylogenetics bioinformatics protein-structure sequence-alignment

Created 2009-03-15

15,828 commits to master branch, last one a day ago

minimap2 lh3

396

1.7k

other

84

A versatile pairwise aligner for genomic and spliced nucleotide sequences

genomics bioinformatics spliced-alignment sequence-alignment

Created 2017-07-18

1,134 commits to master branch, last one 22 days ago

bwa lh3

547

1.5k

gpl-3.0

107

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

fm-index genomics bioinformatics sequence-alignment

Created 2011-01-14

968 commits to master branch, last one about a month ago

diamond bbuchfink

176

981

gpl-3.0

36

Accelerated BLAST compatible local sequence aligner.

sequence-alignment

Created 2015-03-10

2,024 commits to master branch, last one 4 months ago

bwa-mem2 bwa-mem2

91

688

other

35

The next version of bwa-mem

genomics bioinformatics sequence-alignment

Created 2019-02-26

240 commits to master branch, last one about a month ago

vsearch torognes

122

638

other

44

Versatile open-source tool for microbiome analysis

fasta fastq search chimera amplicon clustering microbiome metagenomics metabarcoding bioinformatics sequence-alignment

Created 2014-05-16

1,919 commits to master branch, last one 17 days ago

biojava biojava

380

583

lgpl-2.1

79

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

pdb java genomics bioinformatics parser-library protein-data-bank protein-sequences protein-structure sequence-alignment structure-alignment protein-modification structural-bioinformatics

Created 2013-04-03

6,829 commits to master branch, last one 21 days ago

edlib Martinsos

161

487

mit

22

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

python library c-plus-plus edit-distance alignment-path bioinformatics sequence-alignment levehnstein-distance

Created 2014-01-19

248 commits to master branch, last one about a year ago

minigraph lh3

38

394

mit

28

Sequence-to-graph mapper and graph generator

genomics pan-genome genome-graph bioinformatics sequence-alignment

Created 2019-02-08

611 commits to master branch, last one 22 days ago

seqan3 seqan

80

390

other

24

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

blast cpp17 cpp20 fasta fastq seqan modern fm-index samtools cpp-concepts bioinformatics sequence-analysis sequence-alignment

Created 2016-04-04

6,669 commits to main branch, last one 5 days ago

bistring microsoft

19

368

mit

10

Bidirectionally transformed strings

string sequence-alignment

Created 2019-06-07

144 commits to master branch, last one 7 months ago

miniprot lh3

16

305

mit

7

Align proteins to genomes with splicing and frameshift

bioinformatics sequence-alignment

Created 2022-08-04

249 commits to master branch, last one 3 months ago

sequenceserver wurmlab

112

267

agpl-3.0

19

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

ruby blast genomics javascript sequencing hacktoberfest visualization bioinformatics sequence-alignment genomics-visualization

Created 2010-10-01

2,283 commits to master branch, last one 3 days ago

ksw2 lh3

24

125

other

14

Global alignment and alignment extension

bioinformatics sequence-alignment

Created 2017-06-22

119 commits to master branch, last one 11 months ago

kalign TimoLassmann

28

120

gpl-3.0

6

A fast multiple sequence alignment program.

bioinformatics sequence-analysis sequence-alignment

Created 2019-04-18

401 commits to main branch, last one about a month ago

deepblast flatironinstitute

16

107

bsd-3-clause

6

Neural Networks for Protein Sequence Alignment

protein neural-networks language-modeling protein-sequences protein-structure sequence-alignment structural-alignments

Created 2020-06-04

365 commits to master branch, last one 17 days ago

cogent3 cogent3

53

97

bsd-3-clause

11

Comparative Genomics Toolkit 3

python biology genomics parallel pycogent biopython evolution statistics data-science markov-chain phylogenetics bioinformatics non-stationary signal-processing maximum-likelihood phylogenetic-trees sequence-alignment molecular-evolution biological-sequence-analysis

Created 2019-09-13

8,880 commits to develop branch, last one 16 days ago

orthologr drostlab

27

85

gpl-2.0

12

Genome wide orthology inference and dNdS estimation

Created 2014-07-08

1,087 commits to master branch, last one 8 months ago

unimap lh3

4

85

mit

4

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

genomics bioinformatics sequence-alignment

Created 2020-11-15

47 commits to master branch, last one 3 years ago

pyMSAviz moshi4

10

70

mit

4

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

msa python genomics matplotlib visualization bioinformatics sequence-analysis sequence-alignment multiple-sequence-alignment

Created 2022-11-13

48 commits to main branch, last one 8 months ago

biscuit zhou-lab

24

62

other

8

BISulfite-seq CUI Toolkit

bioinformatics dna-methylation sequence-alignment

Created 2015-06-24

524 commits to master branch, last one 9 months ago

uta biocommons

26

60

apache-2.0

11

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

sequences bioinformatics sequence-alignment

Created 2016-09-09

612 commits to main branch, last one 2 months ago

BioAlignments.jl BioJulia

24

58

mit

18

Sequence alignment tools

biology biojulia bam-files sam-files dna-sequences bioinformatics sequence-analysis sequence-alignment smith-waterman-alignment high-throughput-sequencing

Created 2017-06-15

179 commits to master branch, last one about a year ago

sequence_align kensho-technologies

2

58

apache-2.0

4

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

nlp pyo3 rust python hirschberg bioinformatics needleman-wunsch sequence-alignment natural-language-processing

Created 2023-04-05

17 commits to main branch, last one 26 days ago

Arioc RWilton

8

55

bsd-3-clause

6

Arioc: GPU-accelerated DNA short-read alignment

gpu cuda genomics c-plusplus methylation read-aligners bioinformatics variant-analysis sequence-alignment bisulfite-sequencing dna-sequence-alignment

Created 2014-12-08

187 commits to master branch, last one 9 months ago

minimap2-rs jguhlin

10

51

other

7

Rust bindings to minimap2 library

ffi rust genomics longread minimap2 alignment bioinformatics spliced-alignment sequence-alignment

Created 2022-09-30

379 commits to main branch, last one 6 days ago

miniwfa lh3

3

48

mit

5

A reimplementation of the WaveFront Alignment algorithm at low memory

bioinformatics sequence-alignment

Created 2022-04-01

119 commits to master branch, last one 22 days ago

SneakySnake CMU-SAFARI

11

46

gpl-3.0

9

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 magnit...

gpu fpga edlib minimap2 long-reads short-reads smith-waterman needleman-wunsch sequence-aligner sequence-alignment wavefront-alignment hardware-accelerator pre-alignment-filtering

Created 2019-09-22

73 commits to master branch, last one about a year ago

wfa shenwei356

0

29

mit

3

Wavefront alignment algorithm (WFA) in Golang

wfa golang alignment wavefront sequence-alignment

Created 2024-05-21

42 commits to main branch, last one 3 days ago