Python module that provide an alternative view of the outputs produced by the software pyani

R Code to reproduce results in the Nature Communication paper: Murray, C.S., Gao, Y. & Wu, M. Re-evaluating the evidence for a universal genetic boundary among microbial species. Nat Commun 12, 4059 (2021). https://doi.org/10.1038/s41467-021-24128-2

Rapid, in silico characterization of Bacillus cereus group isolates using WGS data

Bacterial taxonomy construction and evaluation in R

Script for creating a tANI distance matrix for use in phylogenetic reconstruction.

In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data

skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Application and Python module for average nucleotide identity analyses of microbes.

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Approximate nearest neighbour search for microbial genomes based on hash metric