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Related Experiment Video

Updated: Sep 15, 2025

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity.

Martin Larralde^1,2, Georg Zeller^1,2,3, Laura M Carroll^4,5,6,7

¹Structural and Computational Biology Unit, EMBL, 69117 Heidelberg, Germany.

NAR Genomics and Bioinformatics

|July 14, 2025

Summary

New Python libraries simplify prokaryotic species delineation using average nucleotide identity (ANI). These tools offer faster computation and seamless integration into bioinformatics workflows, enhancing genomic analysis.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Average nucleotide identity (ANI) is crucial for prokaryotic species delineation in genomics.
Existing ANI algorithms often lack convenient integration into Python-based bioinformatics workflows.

Purpose of the Study:

To introduce PyOrthoANI, PyFastANI, and Pyskani, Python libraries for popular ANI computation methods.
To facilitate the integration of ANI calculations into Python bioinformatics pipelines.

Main Methods:

Development of three Python libraries: PyOrthoANI, PyFastANI, and Pyskani.
Validation of ANI values against established tools (OrthoANI, FastANI, skani).
Benchmarking of computational speed and multithreading capabilities.

Main Results:

PyOrthoANI, PyFastANI, and Pyskani produce ANI values virtually identical to their command-line counterparts (adjusted R² > 0.999).
PyOrthoANI demonstrates a 3x speed improvement over OrthoANI per genome.
PyFastANI offers multithreading support for single queries.
Libraries integrate seamlessly with BioPython.

Conclusions:

The developed Python libraries provide efficient and convenient tools for ANI computation.
These libraries enhance the usability of popular ANI algorithms within Python bioinformatics workflows.
Open-source availability promotes wider adoption and integration in research.