The envelope glycoproteins, which play a crucial role in virus recognition, invasion and spread. The analysis of the glycosites in HAs and NAs has provided basic information for vaccine design, host selection and changing virulence. However, infection is a complex process; the alternation of glycosites and glycan shapes may affect the functions of glycoproteins. In addition, there are other mutations also worthy of further consideration, such as the E627K in the PB2 protein that enhances the avian viral replication capacity in mammalian cells [76, 77] . Drug resistance is also related to viral proteins, such as the M2 protein [78] . Thus, to prevent the next influenza pandemics, more research needs to be done. Figure S1 The N-J trees of H5N1 HA. The phylogenetic tree was inferred from protein sequences by the Neighbor-Joining method and rooted using A/chicken/Scotland/1959. Estimates of the statistical significance of the phylogenies were calculated by performing 1,000 bootstrap replicates. The clades classified by the WHO are shown as colored bars. (TIF) Figure S2 The superposition of crystal structures from various HA and NA subtypes. The red, green, blue and yellow color represent the H1, H3, H5 and H7 in HAs or N1, N2, N8 and N9 in NA respectively. File S5 The analytic alignment file containing the 5973 protein sequences of H3 HA. As is shown in the output file, the red, green and blue color represent the levels of conservation of ''.95%'', ''5%,95%'' and '',5%'', respectively. (ZIP)