*Non-redundant H5N1, GISAID, Min. Len. 1200 bp, excluding previous sets, non-laboratory derived. **The cleavage site is not included. Start and stop 9-mers with translated amino acids are given for each fragment relative to A/goose/Guangdong/1/96 (AF144305/EPI_ISL_1254); accuracy is the numb: of correct clade annotations over the total number of tested HA nucleotide sequences; BER is the balanced error rate. doi:10.1371/journal.pone.0086921.t001 Table 1. Hemagglutinin clade annotation for avian influenza subtype A(H5N1) by LABEL. Average pairwise distance (APD) values within and between closely related clades using a p-distance calculation with pairwise deletion. The C-value is the ratio of th between group APD to the within group APD. doi:10.1371/journal.pone.0086921.t002 Table 2. Revised 2012 H9IN2 nomenclature. *Named for virus not in our dataset that clusters with clade VN222. doi:10.1371/journal.pone.0086921.t003 Table 3. Revised 2012 H9IN2 nomenclature references. Start and stop 9-mers with translated amino acids are given for each fragment relative to A/chicken/Beijing/1/94 (AF 156380/EPI_ISL_1270); accuracy is the number of correct lineage annotations over the total number of tested HA nucleotide sequences; BER is the balanced error rate. doi:10.1371/journal.pone.0086921.t004 Table 4. Hemagglutinin clade annotation for avian influenza subtype A(H9N2) by LABEL. Figure 3. Two-dimensional scatterplots of profile HMM negative log-likelihood scores for HSN1 hemagglutinins in clades 7 (green circles) and 7.7 (red triangles) along with those in a 7.7-/ike group (blue stars). (A) Plot shows scores for the clade 7.7-specific pHMM (Y-axis) versus scores for the clade 1-specific pHMM (X-axis). (B) As in A, but with the X-axis containing scores for the 1.1-like pHMM instead. Smaller (more negative) numbers are considered better fits for that clade or group. doi:10.1371/iournal.ocone.0086921.q003 Figure 4. Two-dimensional scatterplots of profile HMM negative log-likelihood scores for HSN1 hemagglutinins in clades 3 (greer circles) and 4 (red triangles) along with those in a clade 3-/ike group (blue stars). (A) Plot shows scores for the clade 3-specific pHMM (Y-axis) versus scores for the clade 4-specific pHMM (X-axis). (B) As in A, but with the X-axis containing scores for the 3-like pHMM instead. Smalle (more negative) numbers are considered better fits for that clade or group. doi:10.1371/journal.pone.0086921.g004
