Table 1 Software programs for the reconstruction of GEMs
From: Current status and applications of genome-scale metabolic models
Tool | Language | Graphical user interface (GUI) available? | Source database for metabolic reactions | Use as a reference model? | Gap-filling | Eukaryote modeling | Simulation ready | Reference |
|---|---|---|---|---|---|---|---|---|
AuReMe | Python | No | KEGG, BiGG Models, MetaCyc | No | Yes | Yes | Yes | [87] |
AutoKEGGRec | Matlab | No | KEGG | No | No | No | No | [88] |
CarveMe | Python | No | BiGG Models | Yes (universal model) | Yes | No | Yes | [15] |
CoReCo | Python | No | KEGG | No | Yes | Yes | Yes | [89] |
FAME | Python | Yes | KEGG | Yes | No | No | Yes | [90] |
merlin | Java | Yes | KEGG, MetaCyc, UniProtKB, TCDB | No | No | Yes | No | [91] |
MetaDraft | Python | Yes | BiGG Models | Yes | No | No | Yes | [92] |
Model SEED | Web | Yes | In-house reaction database | Yes | Yes | Yes (only plants) | Yes | [93] |
Pathway Tools | Python, Lisp | Yes | Pathway/Genome Database (PGDB), MetaCyc | No | Yes | Yes | Yes | [94] |
RAVEN 2.0 | Matlab | No | KEGG, MetaCyc | Yes | Yes | Yes | Yes | [95] |
SuBliMinal Toolbox | Java | No | KEGG, MetaCyc | No | No | No | Yes | [96] |