Figure 4.
Summary and representation of the assortment of replicons in CIP 105210T as previously described in [47]. Bars show the relative frequency of functional classes according to the database of clusters of orthologous groups of proteins (COGs). The cluster dendrogram arranges the replicons according to their overall codon usage. Codon-usage matrices were generated using yet unpublished scripts for the statistical analysis software R (version 2.15.0.) [54]. The hierarchical clustering analysis was conducted using the pvclust function [55] with “complete” as agglomeration method. Pvclust also returns the AU (Approximately Unbiased) values as statistical support for clusters in percent. Support values >95% are given in bold. Asterisks indicate the presence of genes for conjugation (T4SS) as listed in Table 7.