Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes

Table 6 Difference between the GTN and SNP-based methods

	GTN method	SNP method
Input file(s)	Fna, faa and gff format files	Gbk format file
Calculation region	Whole genome or common synteny block	Single-copy core genes
Evolutionary evidence	Gene order	SNP
Method for phylogenetic tree	Neighbour-joining	Maximum likelihood
What can be obtained	Neighbour-joining tree; genes at unique node connections; relative DD list; gene indel information; gene clusters (COG); common ancestor information	Maximum likelihood tree; core gene list; core gene alignment result; gene cluster

The SNP-based methods refer to the methods that we used in this study (panX, mafft and RAxML). The information on “genes at unique node connections” includes all genes at unique node connections. All these genes render an altered gene order, and they are evolutionary evidence of genomic evolutionary history (gene indels, duplications and recombination). The results shown in Tab. 2 are mainly based on these results. The information in the “relative DD list” includes all relative DD values of each COG family. The “gene indel” information includes genes in unique COG families or different copies of COG families. “Common ancestor information” includes the average length and number of fragments of a common ancestor; the red numbers in Fig. 3 were based on these results

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