This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Average Nucleotide Identity for 45 genomes

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!

genome sequence alignment
• 3,737 views • link
updated by Ram Ram • written by utkarsh.sood • utkarsh.sood

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

• 0 views • link
updated by Ram Ram • written by 5heikki 5heikki

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

• 0 views • link
written by utkarsh.sood • utkarsh.sood

1 answer

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.

• 0 views • link
written by sentausa sentausa

Log in to answer this question.

More posts like this