Figure 2.

NP PhyloMap. (A) The PhyloMap for 2984 NP protein sequences. Each spot in the plot corresponds to one sequence, and the first two dimensions represent 56.7% of the total variation. The phylogenetic tree mapped onto the plot is shown in (B). The mapping error is 0.00259. The strain names that stand for the numbers in the plot are shown in the phylogenetic tree in (B). (B) The NJ tree of NP protein sequences built using distances inferred by the JTT model; 40 sequences have been selected by PhyloMap as data centers, the other two sequences (in bold italics) have been added manually. This tree has been mapped onto the PCoA result as shown in (A). Bootstrap values (1000 replications) for key nodes are shown. The tree was annotated using "TreeGraph 2" [58]. (C) The relationships of the distances between nodes in the original phylogenetic tree (B) and in the PhyloMap after mapping (A). Correlation coefficient: 0.998. Errors before Bezier curve compensation: 0.0496, after Bezier curve compensation: 0.00259. The errors after Bezier curve compensation are caused by the distances that are longer in the PhyloMap than in the original tree.