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    19 repositories

    • prolipipe

      Public
      The prolific pipeline is about genome annotation and metabolic pathway reconstruction. From .fasta genomes, it enables to find if strains of bacteria are theorically able to produce metabolites
      Python
      •
      GNU General Public License v3.0
      •3•2•0•0•Updated Oct 28, 2025Oct 28, 2025

    • esmecata

      Public
      From taxonomic affiliations to annotated consensus proteomes using UniProt database.
      protein-sequencesuniprottaxonproteomesfunction-estimation
      Python
      •
      GNU General Public License v3.0
      •0•7•0•0•Updated Oct 15, 2025Oct 15, 2025

    • padmet

      Public
      Python library for hAndling metaData of METabolism.
      metabolic-network
      Python
      •
      GNU General Public License v3.0
      •2•6•3•0•Updated Sep 10, 2025Sep 10, 2025

    • aucome

      Public
      Automatic Comparison of Metabolism
      Python
      •
      GNU General Public License v3.0
      •0•6•2•0•Updated Sep 8, 2025Sep 8, 2025

    • metage2metabo-postaviz

      Public
      Shiny app for the analysis of Metage2Metabo's results on multiple community composition
      Python
      •
      GNU Lesser General Public License v3.0
      •0•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • mpwt

      Public
      Pathway Tools multiprocessing wrapper (for PathoLogic).
      multiprocessingmetabolic-networkpathway-tools
      Python
      •
      GNU Lesser General Public License v3.0
      •0•14•5•0•Updated Aug 19, 2025Aug 19, 2025

    • MeReco

      Public
      This is the complete workflow to generate metabolic networks at padmet format from genome fasta files (for now, only bacterial)
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 21, 2025Jul 21, 2025

    • Ontosunburst

      Public
      Sunburst representation of ontologies
      Python
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Jun 19, 2025Jun 19, 2025

    • metage2metabo

      Public
      From annotated genomes to metabolic screening in large scale microbiotas
      bioinformaticsbioinformatics-pipelinemetabolic-models
      Jupyter Notebook
      •
      GNU Lesser General Public License v3.0
      •6•65•7•1•Updated May 16, 2025May 16, 2025

    • emapper2gbk

      Public
      Convert GFF, fastas, annotation table and species name into Genbank.
      Python
      •
      GNU Lesser General Public License v3.0
      •10•16•8•0•Updated May 16, 2025May 16, 2025

    • mpwt-docker

      Public
      A dockerfile for multiprocessing Pathway-Tools.
      pathway-tools
      Dockerfile
      •1•3•0•0•Updated Mar 31, 2025Mar 31, 2025

    • MeneVal

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • aureme

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•3•0•Updated Apr 24, 2024Apr 24, 2024

    • HoloInteract

      Public
      Study interactions hosts and microorganisms at metabolic level.
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 3, 2024Apr 3, 2024

    • padmet-utils

      Public
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Mar 12, 2024Mar 12, 2024

    • aucomana

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

    • wiki-metabolic-network

      Public
      PHP
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 10, 2023May 10, 2023

    • mpwt-singularity

      Public
      Singularity recipe for Pathway-Tools and mpwt.
      pathway-tools
      Singularity
      •0•0•0•0•Updated Apr 27, 2023Apr 27, 2023

    • aureme_docker

      Public
      Makefile
      •0•1•2•0•Updated Oct 26, 2020Oct 26, 2020