soedinglab repositories

58 repositories

hh-suite
Public
Remote protein homology detection suite.
opensource bioinformatics cpp
opensource bioinformatics cpp protein-structure simd alignment profile-search sequence-search hh-suite hhblits
C
•
GNU General Public License v3.0
•152•628•169•6•Updated Oct 7, 2026Oct 7, 2026
MMseqs2-App
Public
MMseqs2 app to run on your workstation or servers
electron docker golang
electron docker golang bioinformatics vue docker-compose profile-search sequence-search mmseqs alphafold2
Vue
•
GNU General Public License v3.0
•34•124•17•11•Updated Oct 2, 2026Oct 2, 2026
spacedust
Public
Discovery of conserved gene clusters in multiple genomes
C
•
GNU General Public License v3.0
•6•135•18•0•Updated Sep 30, 2026Sep 30, 2026
MMseqs2
Public
MMseqs2: ultra fast and sensitive search and clustering suite
bioinformatics taxonomy metagenomics
bioinformatics taxonomy metagenomics alignment sequence-clustering profile-search sequence-search linclust mmseqs blast
C
•
MIT License
•303•2.1k•261•27•Updated Sep 30, 2026Sep 30, 2026
metaeuk
Public
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
bioinformatics metagenomics gene-prediction
bioinformatics metagenomics gene-prediction eukaryotes gene-discovery
C
•
GNU General Public License v3.0
•26•211•30•0•Updated Sep 22, 2026Sep 22, 2026
phylo_grad
Public
Rust
•
Apache License 2.0
•0•5•0•0•Updated Sep 16, 2026Sep 16, 2026
metaeuk-regression
Public
Regression test suite for MetaEuk
Perl
•
GNU General Public License v3.0
•1•0•0•0•Updated Sep 8, 2026Sep 8, 2026
MAGmax
Public
From dereplication to genome enrichment: Enhancing genome recovery across metagenomic samples using MAGmax
Rust
•
GNU General Public License v3.0
•4•37•1•0•Updated Aug 28, 2026Aug 28, 2026
MMseqs2-Regression
Public
MMseqs2 Regression Testing
Shell
•
GNU General Public License v3.0
•6•2•0•3•Updated Aug 21, 2026Aug 21, 2026
MMAD-Risk
Public
Jupyter Notebook
•
Apache License 2.0
•0•1•0•0•Updated Aug 3, 2026Aug 3, 2026
PMGen
Public
peptide-MHC modeling, binding prediction, and protein design.
Jupyter Notebook
•
Apache License 2.0
•4•32•0•3•Updated Jul 24, 2026Jul 24, 2026
LoLalign-analysis
Public
Scripts for Reproducing LoL-align Benchmarks
Jupyter Notebook
•0•3•0•0•Updated Jun 30, 2026Jun 30, 2026
binning_benchmarking
Public
Jupyter Notebook
•0•11•0•0•Updated Apr 14, 2026Apr 14, 2026
b-lore
Public
Bayesian multiple logistic regression for GWAS meta-analysis
C++
•
GNU General Public License v3.0
•2•17•0•1•Updated Aug 20, 2025Aug 20, 2025
hhdatabase_pfam
Public
Scripts to generate the pfam database for hh-suite
Shell
•1•0•2•0•Updated Aug 12, 2025Aug 12, 2025
McDevol
Public
Python
•
GNU General Public License v3.0
•0•8•1•1•Updated Feb 24, 2025Feb 24, 2025
transannot
Public
TransAnnot - a fast transcriptome annotation pipeline
bioinformatics annotation assembly
bioinformatics annotation assembly bioinformatics-pipeline transcriptomics
C
•
GNU General Public License v3.0
•2•20•6•1•Updated Jan 22, 2025Jan 22, 2025
plass
Public
sensitive and precise assembly of short sequencing reads
opensource bioinformatics proteins
opensource bioinformatics proteins metagenomics proteomics sequence-assembler metatranscriptomics
C
•
GNU General Public License v3.0
•15•171•37•0•Updated Oct 11, 2024Oct 11, 2024
WIsH
Public
Predict prokaryotic host for phage metagenomic sequences
C++
•
GNU General Public License v3.0
•9•57•3•0•Updated Sep 17, 2024Sep 17, 2024
pdbx
Public
pdbx is a parser module in python for structures of the protein data bank in the mmcif format
Python
•8•31•2•0•Updated Aug 9, 2024Aug 9, 2024
spacepharer
Public
SpacePHARER CRISPR Spacer Phage-Host pAiRs findER
bioinformatics crispr sequence-analysis
bioinformatics crispr sequence-analysis host-pathogen
C
•
GNU General Public License v3.0
•4•48•7•0•Updated May 8, 2024May 8, 2024
prosstt
Public
PRObabilistic Simulations of ScRNA-seq Tree-like Topologies
Python
•
GNU General Public License v3.0
•9•29•0•2•Updated Jan 10, 2024Jan 10, 2024
CCMpred
Public
Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
C
•
GNU Affero General Public License v3.0
•27•116•19•2•Updated Nov 8, 2023Nov 8, 2023
cooperative_rbp
Public
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Sep 13, 2023Sep 13, 2023
art_marzooplclk
Public
Accompanying repository for the publication "RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton"
bioinformatics
bioinformatics
R
•
MIT License
•0•0•0•0•Updated Jan 4, 2023Jan 4, 2023
tejaas
Public
Tejaas - a tool for discovering trans-eQTLs
gene-expression gtex eqtl
gene-expression gtex eqtl eqtl-mapping trans-eqtl reverse-regression
C
•
GNU General Public License v3.0
•0•12•2•0•Updated Oct 14, 2022Oct 14, 2022
CoCo
Public
Consensus Correction
C++
•
GNU General Public License v3.0
•1•2•0•0•Updated Apr 23, 2022Apr 23, 2022
bmf-webserver
Public
Web server for Bipartite Motif Finder (BMF)
Python
•
GNU Affero General Public License v3.0
•0•0•0•0•Updated Jan 16, 2022Jan 16, 2022
contactpred-felsenstein
Public
Felsenstein implementation for phylogeny correction
C
•
GNU General Public License v3.0
•0•0•1•0•Updated Aug 29, 2021Aug 29, 2021
CCMgen
Public
dca contact-prediction
dca contact-prediction
HTML
•
GNU Affero General Public License v3.0
•9•20•5•1•Updated Jul 16, 2021Jul 16, 2021

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Söding Lab

All

58 repositories

hh-suite

MMseqs2-App

spacedust

MMseqs2

metaeuk

phylo_grad

metaeuk-regression

MAGmax

MMseqs2-Regression

MMAD-Risk

PMGen

LoLalign-analysis

binning_benchmarking

b-lore

hhdatabase_pfam

McDevol

transannot

plass

WIsH

pdbx

spacepharer

prosstt

CCMpred

cooperative_rbp

art_marzooplclk

tejaas

CoCo

bmf-webserver

contactpred-felsenstein

CCMgen

Repositories list

58 repositories