Phylogenetic relationships among the core genes of Bacillaceae and Enterobacteriaceae . (A) Phylogenetic trees of the concatenated core sequences that were constructed using the neighbor-joining (NJ) method (by CLUSTALW) and the maximum likelihood (ML) method (by MOLPHY). On the branch with an asterisk, the program did not assign any bootstrap value. (B) Phylogenetic networks of the concatenated core sequences constructed using the NeighborNet method (by SplitsTree). (C) Multidimensional scaling analysis of the phylogenetic tree topologies of the individual core genes. A tree topology is represented as a filled circle whose area is proportional to the number of occurrences and whose color indicates the distance from the ML tree topology of the concatenated core sequences (A), which itself is represented as a red circle. The topologies of the 16S and 23S rRNAs are also indicated by arrows.