| Summary: | In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. Here, we are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.FBA, Flux Balance Analysis; GEM, genome-scale metabolic model; GPR, gene\textendashprotein\textendashreaction association; GUI, graphical user interfaces; KBase, DOE Systems Biology Knowledgebase; LP, linear programing; MILP, Mixed-Integer Linear Programing; SBML, Systems Biology Markup Language
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