Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes
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This perl script calculates average nucleotide identity (ANI) for a pair of prokaryotic genomes. ANI has been used by microbial community to measure genetic distance of prokaryotes. This perl script is developed based on algorithm described in the article “Richter, M. and R. Rossello-Mora (2009). "Shifting the genomic gold standard for the prokaryotic species definition." Proc Natl Acad Sci U S A 106(45): 19126-19131.”
The authors of this article have developed JSpecies ( for calculating ANI, but the software runs only on graphical user interface. First, we found it time consuming when it comes to calculate ANI for hundreds of strains using JSpecies, since we need many clicks on the graphical user interface.  Second, most of our genome data is stored in our local computing cluster. It will be more convenient to run ANI in Linux shell commands. Therefore this perl script is developed.
The script has been tested on some random selected strains, and results were consistent with JSpecies.