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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]