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NOTE: this wiki describes BackBLAST v1, which is no longer being maintained. BackBLAST v2 beta, which is described in the README for this repo, is the current active version. The BackBLAST algorithm page still accurately describes the algorithm performed by backblast search, however.

This repository contains a reciprocal BLAST program for filtering down BLAST results to best bidirectional hits. It also contains a toolkit for finding and visualizing BLAST hits for gene clusters within multiple bacterial genomes.

• [BackBLAST.py] (https://github.com/LeeBergstrand/BackBLAST-Gene-Cluster-Finder/wiki/BackBLAST.py) - A script that uses NCBI BLAST to search for gene clusters across multiple genomes. Non-orthalagous genes are filtred out by identifying and extracting only Bidirectional Best BLAST Hits using a [graph-based algorithm] (https://github.com/LeeBergstrand/BackBLAST-Gene-Cluster-Finder/wiki/BackBLAST-Algorithm).
• Visualization - This repository also includes tools for visualizing the results of BackBLAST.py in the form of a R heat map.
• It also contains a submodule that will help you gather 16S genes for building a phylogenetic tree that can be used to organize the bacteria in your heatmap.