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The best evolutionary model was estimated with GARLI software (i.e., general time reversible + Γ + I model).
The nucleotide and AA maximum likelihood trees were generated based on the general time reversible and JTT substitution models respectively.
The data set was analyzed by maximum-likelihood using RAxML31) applying the General Time Reversible model of nucleotide substitution.
The analysis used a General Time Reversible model (GTR) with Gamma distribution for modeling site heterogeneity and base frequencies estimated from the data.
General time reversible (GTR + I + G) was the nucleotide substitution model selected.
The general time reversible (GTR) nucleotide substitution model with gamma distribution was chosen to calibrate the nucleotide substitution rate.
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We used a general time-reversible substitution model with gamma rate variation.
The General Time-Reversible (GTR) model was used with a gamma parameter of 4 and invariant sites.
The maximum likelihood tree was created via a gamma-corrected, general time-reversible model in GARLI [52].
A phylogenetic tree of the 481 hemagglutinin sequences was constructed via gamma-corrected, general time-reversible maximum likelihood (Figure S1).
The general time-reversible (GTR) model with invariant sites (I) with four rate categories had maximum likelihood.
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