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OAT
Welcome to ChunLab's Orthologous Average Nucleotide Identity Tool (OAT),
a similarity measurement tool for genomes.

Overview

OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be integrated into preexisting bioinformatics pipelines.

Update Notes
(2015-10-26) GGDC calculator is updated (http://ggdc.dsmz.de/), calculating GGDC1, GGDC2, and GGDC3.
(2017-06-14) User can now specify the number of worker threads.

Input

Genome FASTA files.

Output

CSV file.

Citing this software

Lee, I., Kim, Y. O., Park, S. C., & Chun, J. (2015). OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. [Full Text]

Requirements

  • Java Runtime Environment Version 8 (Java Download)
  • NCBI BLAST is required if you are using the Runnable JAR version of OAT. We recommend ncbi-blast-2.2.30+ or higher since OAT was tested with ncbi-blast-2.2.30+ (BLAST+ executables)

Download OAT

  • OAT standalone
OAT Runnable JAR Download 64 bit
OAT for Windows OSDownload 64 bit
OAT User ManualDownload PDF
  • OAT command line
OAT CMD JARDownload 64 bit
OAT CMD Manual Download PDF

Additional Resources

  • Example Genome Sets
Klebsiella SetDownload zip
Mycoplasma Set Download zip

License

OAT can be used without any restriction. However, its redistribution in any way, form, shape, or derivative is strictly prohibited.

Screenshots

Handling input FASTA files
Result screen #1 Table
Result screen #2 Matrix
Result screen #3 Heatmap

Tutorial video

Support

If you experience any difficulties or have questions about the OAT application, please reach out to us at lebmaster.snu+oat.help@gmail.com

Developers

Yeong Ouk Kim

Yeong Ouk Kim received his B.S. in Computer Science and Applied Statistics at Purdue University (2012) and is currently a MS-Ph.D candidate in Bioinformatics at Seoul National University.
Imchang Lee

Imchang Lee is currently a MS-Ph.D candidate in Bioinformatics at Seoul National University.
Sang-Cheol Park

Sang-Cheol Park received his B.S. at Seoul National University and is currently a MS-Ph.D candidate in Bioinformatics at Seoul National University.
Jongsik Chun

Jongsik Chun is a professor at Seoul National University and specializes in microbial evolution, bioinformatics, and genomics. He has been a trustee of Bergey’s Manual Trust since 2010 and is also the founder of ChunLab, Inc.