Running Roary with a bacterial genus

[valeriamateo]

Hi!

I would like to use Roary with genomes of the same bacterial genus and I want to know if this is a suitable option for a dataset with many different bacterial species. I already ran Roary with my dataset and I modified the identity to a lower value (60%). I had no problem while running the program but I don´t know if I can trust the results because I´m aware it is appropiate to use Roary when the genomes of the dataset belong to the same species. Thank you in advance, I hope you can help me clarify this question.

[YiJessePi]

@valeriamateo I'm currently thinking about the same thing. Any thoughts since you asked?

[tseemann]

I wouldn't trust it. Maybe compare it to other methods like proteinortho and MMseqs2