All

30 repositories

FAMSA
Public
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
bioinformatics proteomics longest-common-subsequence
bioinformatics proteomics longest-common-subsequence pfam multiple-sequence-alignment sequence-similarity guide-tree
C++
•
GNU General Public License v3.0
•33•246•11•2•Updated Apr 15, 2026Apr 15, 2026
agc
Public
Assembled Genomes Compressor
compression genomes
compression genomes
C++
•
MIT License
•16•179•8•3•Updated Mar 26, 2026Mar 26, 2026
mdcompress
Public
C++
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Mar 25, 2026Mar 25, 2026
KMC
Public
Fast and frugal disk based k-mer counter
C++
•83•329•96•5•Updated Mar 10, 2026Mar 10, 2026
clusty
Public
clustering leiden sparse-matrices
clustering leiden sparse-matrices cd-hit set-cover single-linkage complete-linkage uclust
C++
•
GNU General Public License v3.0
•4•15•2•1•Updated Jan 28, 2026Jan 28, 2026
protestar
Public
Protein Structure Archiver
compression proteins pdb
compression proteins pdb mmcif alphafold
C++
•
GNU General Public License v3.0
•0•14•0•0•Updated Sep 10, 2025Sep 10, 2025
SPLASH
Public
C++
•
GNU General Public License v3.0
•14•85•29•2•Updated Sep 4, 2025Sep 4, 2025
microbialSPLASH
Public
Python
•
MIT License
•0•0•0•0•Updated Jul 14, 2025Jul 14, 2025
vclust
Public
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
clustering viruses taxonomic-classification
clustering viruses taxonomic-classification dereplication average-nucleotide-identity sequence-similarity genome-sequence bacteriophages
Python
•
GNU General Public License v3.0
•4•109•8•0•Updated May 23, 2025May 23, 2025
kmer-db
Public
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
bioinformatics genomics indexing
bioinformatics genomics indexing k-mer sequence-similarity
C++
•
GNU General Public License v3.0
•18•98•12•0•Updated May 20, 2025May 20, 2025
bkc
Public
C++
•0•1•1•0•Updated May 8, 2025May 8, 2025
ref-utils
Public
C++
•
GNU General Public License v3.0
•0•0•0•0•Updated Dec 5, 2024Dec 5, 2024
LZ-ANI
Public
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
viruses genome-sequencing average-nucleotide-identity
viruses genome-sequencing average-nucleotide-identity sequence-similarity bacteriophages
C++
•
GNU General Public License v3.0
•2•12•1•0•Updated Nov 25, 2024Nov 25, 2024
PHIST
Public
Phage-Host Interaction Search Tool
bioinformatics genomics bacterial-genomes
bioinformatics genomics bacterial-genomes k-mers phages host-prediction
C++
•
GNU General Public License v3.0
•3•30•5•0•Updated Jul 8, 2024Jul 8, 2024
colord
Public
A versatile compressor of third generation sequencing reads.
bioinformatics compression genomics
bioinformatics compression genomics sequencing oxford-nanopore long-reads fastq-files pac-bio
C++
•
GNU General Public License v3.0
•14•53•7•2•Updated Mar 24, 2024Mar 24, 2024
fqsqueezer
Public
FQSqueezer - FASTQ compressor based on k-mer statistics
compression ngs genome-sequencing
compression ngs genome-sequencing illumina short-reads
C++
•0•17•1•0•Updated Feb 24, 2024Feb 24, 2024
RECKONER
Public
C++
•1•9•2•0•Updated Jan 26, 2024Jan 26, 2024
Whisper
Public
C++
•
GNU General Public License v3.0
•4•24•7•1•Updated Jan 25, 2024Jan 25, 2024
DSRC
Public
DSRC - DNA Sequence Reads Compressor
C++
•20•60•14•1•Updated May 20, 2022May 20, 2022
GDC2
Public
Genome Differential Compressor 2
C++
•
GNU General Public License v2.0
•4•8•1•0•Updated May 20, 2022May 20, 2022
TGC
Public
Thousands Genome Compressor
C++
•1•1•0•0•Updated May 19, 2022May 19, 2022
QuickProbs
Public
Accurate algorithm for the multiple sequence alignment.
C++
•1•1•2•0•Updated May 19, 2022May 19, 2022
MuGI
Public
Multiple Genome Index
C++
•
GNU General Public License v2.0
•1•1•1•0•Updated May 19, 2022May 19, 2022
CoMSA
Public
Compressor of multiple sequence alignments data
C
•0•6•1•0•Updated May 19, 2022May 19, 2022
GTC
Public
GenoTypes Compressor
C++
•
GNU General Public License v3.0
•8•16•2•0•Updated May 19, 2022May 19, 2022
GTShark
Public
GTShark: Genotype compression in large projects
C++
•
GNU General Public License v3.0
•4•3•2•0•Updated May 19, 2022May 19, 2022
VCFShark
Public
C++
•
GNU General Public License v3.0
•1•18•1•1•Updated May 19, 2022May 19, 2022
ORCOM
Public
Overlapping Reads COmpression with Minimizers
C++
•
GNU General Public License v2.0
•4•16•1•0•Updated May 19, 2022May 19, 2022
FaStore
Public
FaStore - high-performance FASTQ files compressor
C++
•
GNU General Public License v3.0
•7•19•4•0•Updated May 19, 2022May 19, 2022
RADULS
Public
Ultra fast MSD radix sorter
C++
•
GNU General Public License v3.0
•5•10•1•1•Updated Jun 23, 2020Jun 23, 2020

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REFRESH Bioinformatics Group

All

All

30 repositories

FAMSA

agc

mdcompress

KMC

clusty

protestar

SPLASH

microbialSPLASH

vclust

kmer-db

bkc

ref-utils

LZ-ANI

PHIST

colord

fqsqueezer

RECKONER

Whisper

DSRC

GDC2

TGC

QuickProbs

MuGI

CoMSA

GTC

GTShark

VCFShark

ORCOM

FaStore

RADULS

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All

Repositories list

30 repositories