pyANI-plus

Author

Angelika Kiepas, Peter Cock, and Leighton Pritchard

Published

March 15, 2025

About pyANI-plus

pyANI-plus is a Python package and software package that calculates average nucleotide identity (ANI), provides other related measures for whole genome comparisons, stores results persistently in a local SQLite3 database, and renders relevant graphical and tabular summary output. It is designed to be used with draft or complete prokaryote genomes, and implements the following methods:

  • ANIb (average nucleotide identity using BLAST+)
  • ANIm (average nucleotide identity using MUMmer)
  • dnadiff (average nucleotide identity using dnadiff)
  • fastANI (average nucleotide identity using fastANI)
  • sourmash (average nucleotide identity using sourmash)
  • external-alignment (pairwise average nucleotide identity from an externally-generated multiple sequence alignment)

In addition to calculating ANI for a given set of genomes, pyANI-plus also includes the following features:

  • Plotting heatmaps and distributions for individual runs.
  • Comparing and visualising multiple runs.
  • Exporting any single run from the pyANI-plus SQLite3 database in tabular format.
  • Classifying genomes into clusters based on ANI results.
  • Resuming partial runs already logged in the database.
  • Deleting any single run from the pyANI-plus SQLite3 database.
  • Running on a High Performance Compute (HPC) cluster.