ModelSEED v2 manuscript data: reconstruction templates, core models, comparison models, tables and figures

Data accompanying the manuscript "ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction." The dataset includes the ModelSEED v5 reconstruction templates used in the study, core metabolic models, CarveMe comparison models, five supplementary tables, four supplementary figures, and a manifest with file sizes and checksums. The study evaluates ModelSEED v2 across bacterial and archaeal genomes, including ATP production across 54 media formulations, comparison with CarveMe, comparison with the legacy ModelSEED pipeline, and gap-filling in glucose minimal and auxotrophy media. Supplementary Data S2 and S3 contain the model collections generated during the study. Individual analyses used subsets of these collections: 5,540 core models and 5,420 genome-scale models. Models outside these sets were not included in the reported summary statistics or figures. Current ModelSEED software is available through https://modelseed.org/ and https://github.com/ModelSEED/modelseed-api.