Nucleotide and amino acid identity calculation

Question

[akbar.shahid]

Hi All,

I have assembled a mycoplasma genome using next generation sequencing and optical map. I want to do some preliminary analysis of my whole genome and few already assembled in database. I want to calculate average nucleotide identity (ANI) and average amino acid identity (AAI). Which program can help in this regard? I used Kostas lab (http://enve-omics.ce.gatech.edu/) to estimate these values but I got errors like "
Insufficient hits to estimate one-way AAI: 0 Insufficient hits to estimate one-way AAI: 0 Insufficient hits to estimate two-way AAI: 0 "

Also, the information they provided was not downloadable due to certain errors. Any suggestion regarding this particular issue would be highly appreciated.

Can anyone suggest how I can calculate these value i.e AAI and ANI?

Thanks in advance.

Shahid

[leaoaniele]

Hi, did You find other way to calculate AAI and ANI?

Answer 1

[LauferVA]

You might try JSpecies.

I would start by reading this short article http://imedea.uib-csic.es/jspecies/about.html then start on the citations that are linked - several of them provide different methods of calculating ANI.