Söding Lab

All

51 repositories

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
•
GNU General Public License v3.0
•195•1.4k•390•12•Updated Oct 29, 2024Oct 29, 2024
transannot
Public
TransAnnot - a fast transcriptome annotation pipeline
bioinformatics annotation assembly bioinformatics-pipeline transcriptomics
C
•
GNU General Public License v3.0
•1•7•0•0•Updated Oct 23, 2024Oct 23, 2024
plass
Public
sensitive and precise assembly of short sequencing reads
opensource bioinformatics proteins metagenomics proteomics sequence-assembler metatranscriptomics
C
•
GNU General Public License v3.0
•14•147•29•0•Updated Oct 11, 2024Oct 11, 2024
spacedust
Public
Discovery of conserved gene clusters in multiple genomes
C
•
GNU General Public License v3.0
•2•55•5•0•Updated Oct 8, 2024Oct 8, 2024
MMseqs2-App
Public
MMseqs2 app to run on your workstation or servers
docker golang bioinformatics vue docker-compose profile-search sequence-search mmseqs alphafold2 colabfold
Vue
•
GNU General Public License v3.0
•18•59•10•9•Updated Sep 19, 2024Sep 19, 2024
WIsH
Public
Predict prokaryotic host for phage metagenomic sequences
C++
•
GNU General Public License v3.0
•10•52•2•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•22•2•1•Updated Aug 9, 2024Aug 9, 2024
metaeuk
Public
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
bioinformatics metagenomics gene-prediction eukaryotes gene-discovery
C
•
GNU General Public License v3.0
•23•177•26•0•Updated Jul 12, 2024Jul 12, 2024
MMseqs2-Regression
Public
MMseqs2 Regression Testing
Shell
•
GNU General Public License v3.0
•3•1•0•1•Updated May 21, 2024May 21, 2024
spacepharer
Public
SpacePHARER CRISPR Spacer Phage-Host pAiRs findER
bioinformatics crispr sequence-analysis host-pathogen
C
•
GNU General Public License v3.0
•4•36•5•0•Updated May 8, 2024May 8, 2024
metaeuk-regression
Public
Regression test suite for MetaEuk
Perl
•
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
•
GNU General Public License v3.0
•11•25•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
•25•106•20•2•Updated Nov 8, 2023Nov 8, 2023
cooperative_rbp
Public
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 13, 2023Sep 13, 2023
hh-suite
Public
Remote protein homology detection suite.
opensource bioinformatics protein-structure simd profile-search sequence-search hh-suite profile-profile-search hhsearch hhpred
C
•
GNU General Public License v3.0
•134•538•157•9•Updated Aug 13, 2023Aug 13, 2023
b-lore
Public
Bayesian multiple logistic regression for GWAS meta-analysis
Python
•
GNU General Public License v3.0
•1•16•1•0•Updated Aug 3, 2023Aug 3, 2023
art_marzooplclk
Public
Accompanying repository for the publication "RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton"
bioinformatics
R
•
MIT License
•0•0•0•0•Updated Jan 4, 2023Jan 4, 2023
tejaas
Public
Tejaas - a tool for discovering trans-eQTLs
gtex eqtl eqtl-mapping reverse-regression gene-expression trans-eqtl
C
•
GNU General Public License v3.0
•0•10•2•0•Updated Oct 14, 2022Oct 14, 2022
CoCo
Public
Consensus Correction
C++
•
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
•
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
HTML
•
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
•
GNU General Public License v3.0
•0•0•0•0•Updated Mar 25, 2021Mar 25, 2021
bipartite_motif_finder
Public
BMF: Bipartite Motif Finder
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Mar 25, 2021Mar 25, 2021
BaMMmotif2
Public
Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.
bioinformatics chip-seq motif-discovery motif-analysis ngs-analysis
C++
•
GNU General Public License v3.0
•5•12•4•0•Updated Feb 1, 2021Feb 1, 2021
hhdatabase_pfam
Public
Scripts to generate the pfam database for hh-suite
Shell
•0•0•1•0•Updated Jan 27, 2021Jan 27, 2021
hhdatabase_cif70
Public
Scripts to generate the pdb70 database for hh-suite on the basis of pdb's mmcif format
Shell
•
GNU General Public License v3.0
•3•7•0•0•Updated Jan 6, 2021Jan 6, 2021
ffindex_soedinglab
Public
C
•
Other
•2•16•6•2•Updated Aug 10, 2020Aug 10, 2020
bamm-benchmark
Public
Scripts and data for generating the benchmarks in the W Ge, et al. paper.
Jupyter Notebook
•
GNU Affero General Public License v3.0
•0•0•0•0•Updated Jul 13, 2020Jul 13, 2020
merlot
Public
Reconstruct the lineage topology of a scRNA-seq differentiation dataset.
HTML
•
GNU General Public License v3.0
•5•18•0•0•Updated Jun 25, 2020Jun 25, 2020