BiG-SCAPE specifications


Unique identifier OMICS_32516
Alternative name Biosynthetic Gene Similarity Clustering and Prospecting Engine
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some GenBank files from the output of antiSMASH with BGC predictions, as well as reference BGCs from the MIBiG repository.
Output data Some files, as well as a visualization that includes multi-locus phylogenies of each Gene Cluster Family made using CORASON.
Output format TSV
Operating system Unix/Linux
Programming languages Python
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Marnix Medema
  • person_outline Francisco Barona-Gomez

Additional information

Publication for Biosynthetic Gene Similarity Clustering and Prospecting Engine

BiG-SCAPE citations


Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

PMCID: 5853187
PMID: 29556550
DOI: 10.1128/mSystems.00182-17

[…] o gene cluster families (GCFs) are key methods to reduce the complexity of sets of thousands of BGCs and provide a bird’s-eye perspective on the underlying biosynthetic diversity (). Our new software BiG-SCAPE (J. Navarro-Muñoz et al., unpublished data; streamlines and optimizes these methods to allow detailed analysis of the relationships betwee […]


Genome based exploration of the specialized metabolic capacities of the genus Rhodococcus

BMC Genomics
PMCID: 5550956
PMID: 28793878
DOI: 10.1186/s12864-017-3966-1

[…] aim was to identify gene clusters that are only present in one or a few strains, which may encode biosynthetic pathways for the production of novel bioactive compounds. For this purpose, we used the BiG-SCAPE software (Navarro-Muñoz, Yeong, Medema et al., in preparation) to construct a sequence similarity network that categorizes the different GCFs, thus providing a powerful visualization of shar […]

BiG-SCAPE institution(s)
Bioinformatics Group, Wageningen University, The Netherlands; Fungal Natural Products Group, Westerdijk Fungal Biodiversity Institute, The Netherlands; Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, México; Department of Chemistry, Northwestern University, Evanston, Illinois, United States; Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK; Novartis Institutes for BioMedical Research, Cambridge, MA, USA; Microbial Genomics and Bioinformatics, Max Planck Institute for Marine Microbiology, Bremen, Germany
BiG-SCAPE funding source(s)
Supported by the Netherlands Organization for Scientific Research (NWO) VENI Grant [863.15.002], the Graduate School for Experimental Plant Sciences (EPS grant); National Institutes of Health Genome to Natural Products Network supplementary award [U01GM110706], CONACyT [grants CBS2017_285746 and 2017_051TAMU]; postdoctoral scholarship 263661; PhD scholarship 204482 , who was also supported by Innovation Secretary of Guanajuato), the National Cancer Institute (NCI) of the National Institutes of Health (NIH) under Award Number F32CA221327 (MWM), the National Institute of General Medical Sciences (NIGMS) under Award Number F32GM120999 (EIP), the National Center for Complementary and Integrative Health (NCCIH) of the NIH under Award Number R01AT009143.

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