| Popis: |
Figure S3. Reference tree used as a backbone for defining hemagglutinin (HA) H1 subtype clades. The defined H1 clades are H1-α (global nomenclature 1A.1 and 1A.1.1, red); H1-β (1A.2, orange); H1-γ2 (1A.3.2, light green); H1-pdm09 (1A.3.3.2, blue); H1-γ (1A.3.3.3, green); H1-δ1 (1B.2.2, navy); H1-δ1a (1B.2.2.1, dark purple); H1-δ1b (1B.2.2.2, light purple); and H1- δ2 (1B.2.1, magenta). Human seasonal sequences are in black. The reference tree was built using FastTree2 v2.1.9 [32] to infer the best-known maximum-likelihood tree implementing a general time reversible model of nucleotide substitution with a CAT model of rate heterogeneity with branch lengths rescaled to optimize the Gamma20 likelihood. (PDF 5 kb) |
