There was a strong overall match between the clustering based on PFGE dendrogram, spa type, ST, or CC of the analyzed isolates (Table 2; Appendix Figure).
The biggest downside of k-means clustering algorithm is the random cluster ordering on the output; however, this information can be indirectly accessed by looking at the average distance between clusters (based on the supplied metric) as well as the number of points in the cluster.
The final layout is produced in two steps: first, the layout of objects in each cluster is computed based on the relationships between objects, then the layout of clusters based on the relationships between the members of the clusters.
We also estimate divergence time between the Northern and Southern lineage and between population clusters based on sequence divergence in the mitochondrial Cyt B gene.
Despite the clear distinction between clusters based on nucleotides, no such distinction is found when comparing amino acid differences.
The GCPV method is, currently, the only genome comparison based method that allows for the characterization of relationships between gene clusters based profiles of individual genes in clusters.
Following Lujan-Soto et al. (2015), we will use a bivariate mixture model to distinguish between different species clusters, based on maximum size (the mean of the 10%% biggest diameter trees) and average diameter growth.
Future analysis could reveal the potential of assigning transition probabilities between clusters based on physiology, which combined with knowledge of the likelihood of death in each state suggests potential methods of steering the physiology away from clusters with high mortality towards clusters associated with safety.
Consequently, it is possible to obtain a notion of distance between two clusters based on Granger causality, i.e., a continuous measure (distance in terms of Granger causality) instead of a discrete measure (presence or absence of an edge).
gingivalis HtpG p18 between clusters based on clinical measures, but no differences in the response to the whole bacterium.
