Repositories list

• afesm-clusters-web

  Public
  Vue

  •

  GNU General Public License v3.0

  •3•1•0•0•Updated May 6, 2025May 6, 2025

• foldseek

  Public
  Foldseek enables fast and sensitive comparisons of large structure sets.

  clusteringprotein-structurealignments+ 1bioinformatics

  C

  •

  GNU General Public License v3.0

  •123•969•113•5•Updated May 4, 2025May 4, 2025

• foldseek-regression

  Public
  Regression test for foldseek

  Shell

  •2•3•0•0•Updated May 4, 2025May 4, 2025

• probeit

  Public
  Design capture probes

  Python

  •

  GNU General Public License v3.0

  •2•9•0•0•Updated Apr 28, 2025Apr 28, 2025

• foldcomp

  Public
  Compressing protein structures effectively with torsion angles

  bioinformaticsprotein-structurecompression

  C++

  •

  GNU General Public License v3.0

  •14•172•26•0•Updated Apr 21, 2025Apr 21, 2025

• foldmason

  Public
  Multiple Protein Structure Alignment at Scale with FoldMason

  bioinformaticsprotein-structuremsa

  C

  •

  GNU General Public License v3.0

  •16•169•16•0•Updated Apr 21, 2025Apr 21, 2025

• afesm-analysis

  Public
  0•1•0•0•Updated Apr 19, 2025Apr 19, 2025

• Metabuli

  Public
  Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

  bioinformaticstaxonomymetagenomics+ 2k-mertaxonomic-classification

  C++

  •

  GNU General Public License v3.0

  •12•136•21•0•Updated Apr 17, 2025Apr 17, 2025

• SeekRank

  Public
  Rank homologous protein sequences based on a regressor trained on experimental measures

  Jupyter Notebook

  •

  MIT License

  •1•10•0•0•Updated Apr 11, 2025Apr 11, 2025

• unicore

  Public
  Universal and efficient core gene phylogeny with Foldseek and ProstT5

  Rust

  •

  GNU General Public License v3.0

  •6•55•3•0•Updated Apr 7, 2025Apr 7, 2025

• foldmason-analysis

  Public
  R

  •0•1•0•0•Updated Apr 7, 2025Apr 7, 2025

• afdb-clusters-web

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•4•1•0•Updated Mar 29, 2025Mar 29, 2025

• alphafold

  Public
  Open source code for AlphaFold.

  Python

  •

  Apache License 2.0

  •2.4k•11•0•2•Updated Mar 18, 2025Mar 18, 2025

• taxoview

  Public
  A Vue.js plugin for generating interactive Sankey diagrams using Kraken report data

  visualizationbioinformaticsvue+ 3taxonomysankeytaxonomic-classification

  Vue

  •

  GNU General Public License v3.0

  •2•8•0•0•Updated Mar 13, 2025Mar 13, 2025

• Metabuli-App

  Public
  HTML

  •

  GNU General Public License v3.0

  •2•30•1•0•Updated Mar 13, 2025Mar 13, 2025

• folddisco

  Public
  Fast indexing and search of discontinuous motifs in protein structures

  bioinformaticsprotein-structuremotif+ 1foldseek

  Rust

  •

  GNU General Public License v3.0

  •3•22•5•0•Updated Feb 24, 2025Feb 24, 2025

• ufcg

  Public
  UFCG: Universal Fungal Core Genes

  genomicsphylogeneticsfungi+ 2marker-gene-analysisbioinformatics

  Java

  •

  GNU General Public License v3.0

  •0•32•21•0•Updated Feb 3, 2025Feb 3, 2025

• foldseek-multimer-analysis

  Public
  Shell

  •1•5•0•0•Updated Feb 1, 2025Feb 1, 2025

• Metabuli-regression

  Public
  Regression tests for Metabuli

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• bfvd-analysis

  Public
  Big Fantastic Virus Database (BFVD): Code used for analyses

  Shell

  •0•2•1•0•Updated Dec 16, 2024Dec 16, 2024

• mmseqs2-gpu-analysis

  Public
  Shell

  •

  MIT License

  •0•9•0•0•Updated Nov 16, 2024Nov 16, 2024

• colabfold-protocol

  Public
  ColabFold protocol

  Jupyter Notebook

  •8•50•2•0•Updated Oct 17, 2024Oct 17, 2024

• ufcg-web

  Public
  UFCG website

  HTML

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jul 2, 2024Jul 2, 2024

• foldseek-analysis

  Public
  Scripts to benchmark and train foldseek

  Jupyter Notebook

  •4•38•9•1•Updated May 22, 2024May 22, 2024

• petasearch

  Public
  🧬 Efficient parallelized peta-scale protein database search

  C

  •

  GNU General Public License v3.0

  •0•41•5•0•Updated Jan 4, 2024Jan 4, 2024

• petasearch-regression

  Public
  C++

  •0•0•0•0•Updated Jan 4, 2024Jan 4, 2024

• afdb-clusters-analysis

  Public
  Scripts to generate and analyze afdb clusters

  Jupyter Notebook

  •0•11•1•0•Updated Sep 15, 2023Sep 15, 2023

• Metabuli-temp

  Public archive
  Taxonomical classifier using AD k-mer

  C++

  •

  GNU General Public License v3.0

  •12•1•0•0•Updated May 30, 2023May 30, 2023

• foldcomp-analysis

  Public
  C

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Feb 20, 2023Feb 20, 2023

• conterminator

  Public
  Detection of incorrectly labeled sequences across kingdoms

  C

  •

  GNU General Public License v3.0

  •7•85•15•1•Updated Oct 25, 2022Oct 25, 2022