Genomes are exactly identical!

[npawarut]

Hello,

I have used Parsnp to generate a core genome alignment for approximately 700 genomes. However, I have encountered several warnings indicating the presence of identical genomes. While these genomes are not exactly the same, they may be highly similar.

Should I be concerned about these warnings, or is this expected behavior?

Thank you.

Best regards,
Pawarut
raxml.out.txt

[bkille]

Hi @npawarut, thanks for opening an issue.

RAxML (or FastTree) is run only on the core genome identified by Parsnp. So it is possible that the core genome of some sequences are identical, especially if the final core region is particularly small.