Computational Approaches for Microalgal Biofuel Optimization: A Review

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)