Average Nucleotide Identity for 45 genomes

Question

[utkarsh.sood]

Hi

I want to calculate average nucleotide identity between 45 genomes. For this I have to make a 2 way matrix having the ANI values for all the 45 genomes. Can anyone please tell me a way to do it in quick and simple way?

Thanks!

[5heikki]

Human genomes? Plant genomes? Yeast genomes? Bacterial genomes? Closely related? Expected synteny of 100%?

[utkarsh.sood]

These are bacterial genomes, from 45 strains of same bacterial species. the expected synteny is between 90-95%

Answer 1

[sentausa]

Have you tried JSpecies? I have used it for a few genomes (close to but less than 20, I guess), so I don't know if it will work with 45 genomes.