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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
  1. aeggNOG-mapper should be run externally by the user
  2. bBidireactional BLASTP is used with template models and BLASTP with databases (KEGG and Metacyc)