reconstrution of acenstral viral sequences

[Liang Wang]

Hi everyone:

    I want to reconstrut an ancestral protein for a specific virus. The sequences were all came from just one virus (sepecis) but with different collection date such as from 2000-2019. I have already removed all sequences with potential recombination events, and some sequences from close related viruses were used as outgroup. Is it suitable to reconstruct ancestral protein sequnece by using ML method implemented in bppsuite?  If it was unsuitable, which method or software was suitable for doing this task?

[Laurent Guéguen]

Dear Liang,

yes it is suitable. Usually we proceed ML fit of the model/tree on the data with bppml, and then ancestral sequence reconstruction with bppancestor.

Cheers,

Laurent

[Liang Wang]

Dear Laurent,

Thank you for your patience. I will try to proceed with your advice.

Best wishes!