# BiG-SCAPE

**Repository Path**: xianghaoDKY/BiG-SCAPE

## Basic Information

- **Project Name**: BiG-SCAPE
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: AGPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2025-01-20
- **Last Updated**: 2025-08-29

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

![License](https://img.shields.io/github/license/medema-group/BiG-SCAPE)
![Conda downloads](https://img.shields.io/conda/dn/bioconda/bigscape?label=Conda%20downloads)
![Test workflow](https://github.com/medema-group/BiG-SCAPE/actions/workflows/run-tests.yml/badge.svg)
![Test workflow](https://github.com/medema-group/BiG-SCAPE/actions/workflows/deploy-docker.yml/badge.svg)
[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B%20%20%E2%97%8B-orange)](https://fair-software.eu)

## _Notes:<br>BiG-SCAPE 2.0 is still in beta. Please submit an issue if you find anything wrong with this release!<br>BiG-SCAPE 2.0 features several updates to input validation and reference usage. We encourage both experienced BiG-SCAPE 1 users as well as new BiG-SCAPE users to read the updated [documentation](https://github.com/medema-group/BiG-SCAPE/wiki)._

# BiG-SCAPE

**BiG-SCAPE** (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by calculating pairwise distances between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.

BiG-SCAPE uses [antiSMASH](https://antismash.secondarymetabolites.org) processed GenBank files, i.e. BGC predictions, as well as reference BGC GenBank files (user-defined and/or [MIBiG](https://mibig.secondarymetabolites.org) repository). BiG-SCAPE outputs tab-delimited output files, a comprehensive SQLite database which stores all the generated results, and a rich HTML visualization that includes the BGC similarity network and [CORASON](https://github.com/nselem/corason)-like, multi-locus phylogenies of each Gene Cluster Family.

In principle, BiG-SCAPE can also be used on any other gene clusters, such as pathogenicity islands, secretion system-encoding gene clusters, or even whole viral genomes.

For installation instructions, see [here](https://github.com/medema-group/BiG-SCAPE/wiki/Installing-and-Running-BiG-SCAPE).

Learn more about BiG-SCAPE in the [wiki](https://github.com/medema-group/BiG-SCAPE/wiki).


![BiG-SCAPE workflow](figures/BiG-SCAPE-CORASON_Fig1_20171122_v01_MM_nocorason.png)


If you find BiG-SCAPE useful, please cite us:

[A computational framework to explore large-scale biosynthetic diversity](https://doi.org/10.1038/s41589-019-0400-9)