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Substitution model for a viral genome in RAxML

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

sequence genome raxml
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updated by Mensur Dlakic Mensur Dlakic • written by mauricio.1313 • mauricio.1313

1 answer

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.

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written by Mensur Dlakic Mensur Dlakic

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