Substitution model for a viral genome in RAxML

Question

[mauricio.1313]

Hi! Which substitution model do you recommend for viral genomes (nucleotides) in RAxML?

I will do the following analysis "Rapid Boostrap + ML"

I think that for the first time it is good to use the GTR model, however, I would like to know your opinions.

Thank you

Answer 1

[Mensur Dlakic]

ModelFinder in IQ-TREE will quickly test many models and tell you which on is objectively the best. You may want to consider using IQ-TREE over RAxML in general.