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
• cdanielmachado / carveme
  CarveMe: genome-scale metabolic model reconstruction
  ☆165Updated 6 months ago
• SysBioChalmers / RAVEN
  The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
  ☆107Updated last month
• SBRG / bigg_models
  The BiGG Models website server
  ☆81Updated 5 years ago
• franciscozorrilla / metaGEM
  An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…
  ☆228Updated 7 months ago
• opencobra / cobrapy
  COBRApy is a package for constraint-based modeling of metabolic networks.
  ☆489Updated last week
• cdanielmachado / reframed
  ReFramed: metabolic modeling package
  ☆58Updated 7 months ago
• SysBioChalmers / GECKO
  Toolbox for including enzyme constraints on a genome-scale model.
  ☆70Updated 4 months ago
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆555Updated 3 months ago
• antismash / antismash
  antiSMASH
  ☆197Updated last week
• SysBioChalmers / Human-GEM
  The generic genome-scale metabolic model of Homo sapiens
  ☆106Updated last week
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆596Updated 10 months ago
• jotech / gapseq
  Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
  ☆174Updated last week
• SysBioChalmers / yeast-GEM
  The consensus GEM for Saccharomyces cerevisiae
  ☆101Updated 3 months ago
• primer3-org / primer3
  Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
  ☆245Updated 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
  ☆401Updated last month
• jclachance / BOFdat
  Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
  ☆27Updated last year
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆384Updated 2 months ago
• WrightonLabCSU / DRAM
  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
  ☆267Updated 2 weeks ago
• micom-dev / micom
  Python package to study microbial communities using metabolic modeling.
  ☆97Updated last week
• MetabolicAtlas / standard-GEM
  The standard for open-source GEMs on GitHub
  ☆19Updated last year
• rcedgar / muscle
  Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, e…
  ☆235Updated 3 months ago
• ModelSEED / ModelSEEDDatabase
  This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…
  ☆59Updated last month
• weizhongli / cdhit
  Automatically exported from code.google.com/p/cdhit
  ☆656Updated 2 years ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆486Updated this week
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆337Updated 2 years ago
• iqtree / iqtree2
  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
  ☆271Updated last week
• ebi-pf-team / interproscan
  Genome-scale protein function classification
  ☆315Updated 2 weeks ago
• EddyRivasLab / hmmer
  HMMER: biological sequence analysis using profile HMMs
  ☆336Updated last month