Average Nucleotide Identity for 45 genomes
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6.1 years ago
utkarsh.sood ▴ 40

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 • 2.5k views
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Human genomes? Plant genomes? Yeast genomes? Bacterial genomes? Closely related? Expected synteny of 100%?
 

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

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6.1 years ago
sentausa ▴ 640

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.

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