Repositories list

• MAGmax

  Public

  soedinglab/MAGmax’s past year of commit activity
  From dereplication to genome enrichment: Enhancing genome recovery across metagenomic samples using MAGmax

  Rust

  •

  GNU General Public License v3.0

  •2•24•0•0•Updated Jan 25, 2026Jan 25, 2026

• MMseqs2-App

  Public
  MMseqs2 app to run on your workstation or servers

  electrondockergolang+ 10bioinformaticsvuedocker-composeprofile-searchsequence-searchmmseqsalphafold2+ 3

  Vue

  •

  GNU General Public License v3.0

  •30•103•15•9•Updated Jan 23, 2026Jan 23, 2026

• phylo_grad

  Public

  soedinglab/phylo_grad’s past year of commit activity
  Jupyter Notebook

  •

  Apache License 2.0

  •0•2•0•1•Updated Jan 22, 2026Jan 22, 2026

• PMGen

  Public
  peptide-MHC modeling, binding prediction, and protein design.

  Python

  •

  Apache License 2.0

  •3•21•0•1•Updated Jan 22, 2026Jan 22, 2026

• spacedust

  Public

  soedinglab/spacedust’s past year of commit activity
  Discovery of conserved gene clusters in multiple genomes

  C

  •

  GNU General Public License v3.0

  •6•123•19•0•Updated Jan 16, 2026Jan 16, 2026

• MMseqs2

  Public
  MMseqs2: ultra fast and sensitive search and clustering suite

  bioinformaticstaxonomymetagenomics+ 7alignmentsequence-clusteringprofile-searchsequence-searchlinclustmmseqsblast

  C

  •

  MIT License

  •264•2k•474•16•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

  •

  GNU General Public License v3.0

  •3•2•0•1•Updated Oct 14, 2025Oct 14, 2025

• metaeuk

  Public

  soedinglab/metaeuk’s past year of commit activity
  MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

  bioinformaticsmetagenomicsgene-prediction+ 2eukaryotesgene-discovery

  C

  •

  GNU General Public License v3.0

  •24•201•27•0•Updated Aug 25, 2025Aug 25, 2025

• b-lore

  Public

  soedinglab/b-lore’s past year of commit activity
  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

  •0•0•2•0•Updated Aug 12, 2025Aug 12, 2025

• hh-suite

  Public
  Remote protein homology detection suite.

  opensourcebioinformaticscpp+ 11protein-structuresimdalignmentprofile-searchsequence-searchhh-suitehhblits+ 4

  C

  •

  GNU General Public License v3.0

  •149•610•169•7•Updated Aug 12, 2025Aug 12, 2025

• binning_benchmarking

  Public
  Jupyter Notebook

  •0•10•0•0•Updated Jul 31, 2025Jul 31, 2025

• McDevol

  Public
  Python

  •

  GNU General Public License v3.0

  •0•6•1•1•Updated Feb 24, 2025Feb 24, 2025

• transannot

  Public
  TransAnnot - a fast transcriptome annotation pipeline

  bioinformaticsannotationassembly+ 2bioinformatics-pipelinetranscriptomics

  C

  •

  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

  opensourcebioinformaticsproteins+ 4metagenomicsproteomicssequence-assemblermetatranscriptomics

  C

  •

  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++

  •

  GNU General Public License v3.0

  •10•53•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

  bioinformaticscrisprsequence-analysis+ 1host-pathogen

  C

  •

  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

  •

  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

  •9•26•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

  •28•112•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

• 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

  gene-expressiongtexeqtl+ 3eqtl-mappingtrans-eqtlreverse-regression

  C

  •

  GNU General Public License v3.0

  •0•11•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
  dcacontact-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