Alternatives and similar repositories for cobratoolbox:

Users that are interested in cobratoolbox are comparing it to the libraries listed below

• opencobra / memote
  memote – the genome-scale metabolic model test suite
  ☆131Updated last year
• SysBioChalmers / RAVEN
  The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
  ☆108Updated 3 months ago
• SysBioChalmers / yeast-GEM
  The consensus GEM for Saccharomyces cerevisiae
  ☆108Updated 3 weeks ago
• opencobra / cobrapy
  COBRApy is a package for constraint-based modeling of metabolic networks.
  ☆497Updated last month
• SysBioChalmers / Human-GEM
  The generic genome-scale metabolic model of Homo sapiens
  ☆110Updated last week
• cdanielmachado / carveme
  CarveMe: genome-scale metabolic model reconstruction
  ☆165Updated last week
• franciscozorrilla / metaGEM
  An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…
  ☆236Updated 9 months ago
• SysBioChalmers / GECKO
  Toolbox for including enzyme constraints on a genome-scale model.
  ☆70Updated 2 weeks ago
• SysBioChalmers / ecModels
  A container for all enzyme constrained models created by GECKO.
  ☆11Updated 2 years ago
• SBRG / bigg_models
  The BiGG Models website server
  ☆82Updated 5 years ago
• biosustain / cameo
  cameo - computer aided metabolic engineering & optimization
  ☆115Updated 2 years ago
• antismash / antismash
  antiSMASH
  ☆205Updated this week
• jotech / gapseq
  Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
  ☆178Updated this week
• micom-dev / micom
  Python package to study microbial communities using metabolic modeling.
  ☆97Updated last week
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆610Updated 11 months ago
• BioSystemsUM / troppo
  Reconstruction algorithms for Python
  ☆24Updated 6 months ago
• ModelSEED / ModelSEEDDatabase
  This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…
  ☆60Updated 2 months ago
• jclachance / BOFdat
  Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
  ☆27Updated last year
• cdanielmachado / reframed
  ReFramed: metabolic modeling package
  ☆58Updated 2 weeks ago
• VoigtLab / dnaplotlib
  DNA plotting library for Python
  ☆295Updated last year
• hyattpd / Prodigal
  Prodigal Gene Prediction Software
  ☆483Updated last year
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆334Updated this week
• WrightonLabCSU / DRAM
  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
  ☆277Updated 3 weeks ago
• MetabolicAtlas / standard-GEM
  The standard for open-source GEMs on GitHub
  ☆19Updated last year
• zakandrewking / escher
  Build, share, and embed visualizations of metabolic pathways.
  ☆222Updated 8 months ago
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆523Updated 2 months ago
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆567Updated 5 months ago
• shenwei356 / taxonkit
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆409Updated last week
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆505Updated last month
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆454Updated last week