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Table 1 Feature comparison of several tools for metabolic network analysis.

From: OptFlux: an open-source software platform for in silico metabolic engineering


Other tools






File formats/standards



- Metatool format


- Flat files

Phenotype simulation


- FBA: wild type, environmental conditions, gene deletion mutants

- Dynamic FBA









- MFA basic methods


- Gene-reaction associations



- Regulatory network simulation



Strain optimization


- OptKnock algorithm


- Metaheuristics: OptGene


Metabolic Network Analysis


- Elementary Flux Modes


- Minimal cut sets



- Flux Variability Analysis (FVA)

- Topological network analysis






- Built-in visualization


- Interaction with CellDesigner


- Interaction with Cytoscape



Other features


- Graphical user interface


- Does not depend on commercial software


- User documentation

  1. Notes
  2. (1) Implementation based on linear programming formulation (linear MOMA)
  3. (2) Plug-ins under development
  4. (3) Includes some basic graph analysis methods
  5. The table provides a comparison of the main features of OptFlux with the major alternatives in metabolic network analysis. Features have divided into six groups: file formats and standards, phenotype simulation, strain optimization, network analysis, visualization and other features.