Table 2.
Selected software for genome-scale metabolic reconstruction (adapted from Liao et al., 2012 [27]; Agren et al., 2013 [33]; and Hamilton and Reed, 2014 [34]).
| RAVEN | Model SEED | SuBliMinal | GEMSiRV | Pathway Tools | COBRA toolbox | |
|---|---|---|---|---|---|---|
| Input | Annotated genome sequence | Genome annotated in RAST | Species name | Model in sbml format | Annotated genome sequence | Model in sbml format |
|
| ||||||
| Reference databases | KEGG | SEED | KEGG, MetaCyc | KEGG | MetaCyc | N/A |
|
| ||||||
| Interface | MatLab | Web | Command line | Software | Web, software | MatLab |
|
| ||||||
| License | Free (requires a MatLab license) | Free | Free | Free | Free for academic and government use | Free (requires a MatLab license) |
|
| ||||||
| Simulation | Yes | Yes | No | Yes | Yes | Yes |
|
| ||||||
| Visualization | Yes | Yes (with Cytoscape plug-in) | No | Yes | Yes | Yes (with plug-in) |