Söding Lab

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57 repositories

phylo_grad
Public
Jupyter Notebook
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Apache License 2.0
•0•1•0•1•Updated Dec 20, 2025Dec 20, 2025
PMGen
Public
peptide-MHC modeling, binding prediction, and protein design.
Python
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Apache License 2.0
•3•19•0•1•Updated Dec 19, 2025Dec 19, 2025
MMseqs2-App
Public
MMseqs2 app to run on your workstation or servers
electron docker golang bioinformatics vue docker-compose profile-search sequence-search mmseqs alphafold2
Vue
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GNU General Public License v3.0
•29•101•15•10•Updated Dec 19, 2025Dec 19, 2025
MAGmax
Public
From dereplication to genome enrichment: Enhancing genome recovery across metagenomic samples using MAGmax
Rust
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GNU General Public License v3.0
•2•23•0•0•Updated Dec 18, 2025Dec 18, 2025
MMseqs2
Public
MMseqs2: ultra fast and sensitive search and clustering suite
bioinformatics taxonomy metagenomics alignment sequence-clustering profile-search sequence-search linclust mmseqs blast
C
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MIT License
•262•1.9k•474•15•Updated Dec 5, 2025Dec 5, 2025
LoLalign-analysis
Public
Scripts for Reproducing LoL-align Benchmarks
Jupyter Notebook
•0•1•0•0•Updated Nov 21, 2025Nov 21, 2025
MMseqs2-Regression
Public
MMseqs2 Regression Testing
Shell
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GNU General Public License v3.0
•3•2•0•1•Updated Oct 14, 2025Oct 14, 2025
metaeuk
Public
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
bioinformatics metagenomics gene-prediction eukaryotes gene-discovery
C
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GNU General Public License v3.0
•24•201•27•0•Updated Aug 25, 2025Aug 25, 2025
b-lore
Public
Bayesian multiple logistic regression for GWAS meta-analysis
C++
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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
•0•0•2•0•Updated Aug 12, 2025Aug 12, 2025
hh-suite
Public
Remote protein homology detection suite.
opensource bioinformatics cpp protein-structure simd alignment profile-search sequence-search hh-suite hhblits
C
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GNU General Public License v3.0
•148•608•169•7•Updated Aug 12, 2025Aug 12, 2025
binning_benchmarking
Public
Jupyter Notebook
•0•10•0•0•Updated Jul 31, 2025Jul 31, 2025
spacedust
Public
Discovery of conserved gene clusters in multiple genomes
C
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GNU General Public License v3.0
•6•119•18•0•Updated May 16, 2025May 16, 2025
McDevol
Public
Python
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GNU General Public License v3.0
•0•6•1•1•Updated Feb 24, 2025Feb 24, 2025
transannot
Public
TransAnnot - a fast transcriptome annotation pipeline
bioinformatics annotation assembly bioinformatics-pipeline transcriptomics
C
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GNU General Public License v3.0
•1•20•4•0•Updated Jan 22, 2025Jan 22, 2025
plass
Public
sensitive and precise assembly of short sequencing reads
opensource bioinformatics proteins metagenomics proteomics sequence-assembler metatranscriptomics
C
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GNU General Public License v3.0
•15•163•37•0•Updated Oct 11, 2024Oct 11, 2024
WIsH
Public
Predict prokaryotic host for phage metagenomic sequences
C++
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GNU General Public License v3.0
•10•52•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
•7•30•2•0•Updated Aug 9, 2024Aug 9, 2024
spacepharer
Public
SpacePHARER CRISPR Spacer Phage-Host pAiRs findER
bioinformatics crispr sequence-analysis host-pathogen
C
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GNU General Public License v3.0
•4•44•7•0•Updated May 8, 2024May 8, 2024
metaeuk-regression
Public
Regression test suite for MetaEuk
Perl
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GNU General Public License v3.0
•1•0•0•0•Updated May 1, 2024May 1, 2024
prosstt
Public
PRObabilistic Simulations of ScRNA-seq Tree-like Topologies
Python
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GNU General Public License v3.0
•9•26•0•2•Updated Jan 10, 2024Jan 10, 2024
CCMpred
Public
Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
C
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GNU Affero General Public License v3.0
•28•112•20•2•Updated Nov 8, 2023Nov 8, 2023
cooperative_rbp
Public
Python
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GNU General Public License v3.0
•0•0•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
R
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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 eqtl-mapping trans-eqtl reverse-regression
C
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GNU General Public License v3.0
•0•11•2•0•Updated Oct 14, 2022Oct 14, 2022
CoCo
Public
Consensus Correction
C++
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GNU General Public License v3.0
•0•1•0•0•Updated Apr 23, 2022Apr 23, 2022
bmf-webserver
Public
Web server for Bipartite Motif Finder (BMF)
Python
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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
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GNU General Public License v3.0
•0•0•1•0•Updated Aug 29, 2021Aug 29, 2021
CCMgen
Public
dca contact-prediction
HTML
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GNU Affero General Public License v3.0
•10•20•5•1•Updated Jul 16, 2021Jul 16, 2021
bmf-paper
Public
Notebooks to reproduce the analyses in BMF manuscript
Jupyter Notebook
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GNU General Public License v3.0
•0•0•0•0•Updated Mar 25, 2021Mar 25, 2021