Analysing viral sequences

[a-qvecell]

Hello,
I came across Gubbins when looking for a tool suitable for analysing our dataset of around 350 closely related viral coronavirus sequences with a length of approx. 30.000 bp(not SARS-CoV-2). On average, their diversity is around 1,3 % with a maximum of around 11 %.

I see you suggest to change the window size if studying viral sequences, but I am wondering if Gubbins is the right tool considering the above.

Do you have any advise?
Thank you in advance.
Best wishes,
Amanda