I would like to know which substitution model is being used to construct phylogenetic trees for seasonal influenza A H3N2. From the core.smk at snakemake rules and nextstrain-public.yaml at profiles, I concluded that IQ-Tree is being used with arguments (-ninit 10 -n 4 -czb) but it is not clear to me which substitution model is being used.
For context, I am new to phylogenetic trees and want to explore the right way to construct such trees for seasonal influenza A H3N2 virus isolates.
Hi @sawshah and welcome to the forum! The default substitution model for augur tree with IQ-TREE is the GTR model. This information isn’t exposed directly in the seasonal-flu workflow, but you can find these types of details in the Augur documentation (for example: augur tree documentation) or by running a specific augur command from the command line with the -h flag (e.g., augur tree -h).
We don’t currently provide a way to override the default IQ-TREE substitution model with a different model in the seasonal-flu workflow tree rule, but if that type of functionality would be useful, we could easily add it.