* [http://bioinformatics.ai.sri.com/ptools/ Pathway Tools]: A bioinformatics software package that assists in the construction of pathway/genome databases such as EcoCyc. Developed by Peter Karp and associates at the SRI International Bioinformatics Research Group, Pathway Tools has several components. Its PathoLogic module takes an annotated genome for an organism and infers probable metabolic reactions and pathways to produce a new pathway/genome database.  Its MetaFlux component can generate a quantitative metabolic model from that pathway/genome database using flux-balance analysis.  Its Navigator component provides extensive query and visualization tools, such as visualization of metabolites, pathways, and the complete metabolic network.
* [http://ergo.integratedgenomics.com/ ERGO]: A subscription-based service developed by Integrated Genomics. It integrates data from every level including genomic, biochemical data, literature, and high-throughput analysis into a comprehensive user friendly network of metabolic and nonmetabolic pathways.
* [http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/ KEGGtranslator]: an easy-to-use stand-alone application that can visualize and convert KEGG files (KGML formatted XML-files) into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts these files to SBML, BioPAX, SIF, SBGN, SBML with qualitative modeling extension, GML, GraphML, JPG, GIF, LaTeX, etc.
* [http://modelseed.org/ ModelSEED]: An online resource for the analysis, comparison, reconstruction, and curation of genome-scale metabolic models. Users can submit genome sequences to the RAST annotation system, and the resulting annotation can be automatically piped into the ModelSEED to produce a draft metabolic model. The ModelSEED automatically constructs a network of metabolic reactions, gene-protein-reaction associations for each reaction, and a biomass composition reaction for each genome to produce a model of microbial metabolism that can be simulated using Flux Balance Analysis.
* MetaMerge: algorithm for semi-automatically reconciling a pair of existing metabolic network reconstructions into a single metabolic network model.
* [https://github.com/esaskar/CoReCo CoReCo]: algorithm for automatic reconstruction of metabolic models of related species. The first version of the software used KEGG as reaction database to link with the EC number predictions from CoReCo. Its automatic gap filling using atom map of all the reactions produce functional models ready for simulation.