Table 1 List of selected genome-scale metabolic reconstruction tools and their main features
From: A systematic assessment of current genome-scale metabolic reconstruction tools
Reconstruction tool | Mapping method | Reactions are inherited from | Associated databases | Version | Type of software |
|---|---|---|---|---|---|
AuReMe | Pantograph (Inparanoid and OrthoMCL) | Template model(s) | BIGG-MetaCyc | 1.2.4 | Command line |
CarveMe | Diamond, eggNOG-mappera | Template model | BIGG | 1.2.1 | Command line |
Merlin | Mapping from annotation with BLAST or HMMER | Database | KEGG | 3.8 | Standalone interface |
MetaDraft | Autograph (Inparanoid) | Template model(s) | BIGG | 0.9.2 | Standalone interface |
ModelSEED | Annotation ontology map from RAST data | Template model | ModelSEED | 2.2–2.4 | Online service |
Pathway Tools | Pathologic | Database | MetaCyc | 22.0 | Standalone interface |
RAVEN | Autograph-type method from BLASTP and Bidirectional BLASTPb | Database- Template model(s) | KEGG-MetaCyc | 2.0.1 | Command line |