Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

Table 1 Methods, thresholds and reference genomes for inference of phylogeny for all 101 sequenced strains

Method	Tree name	Reference genome	Threshold 1	Threshold 2	Tree method
CSI Phylogeny	CSI_all_1	Assembled contigs from root sample	Z-score 1.96	Prune disabled	FastTree
CSI Phylogeny	CSI_all_2	Assembled contigs from root sample	Z-score 1.96	Prune set to 10	FastTree
CSI Phylogeny	CSI_all_3	E. coli NC_000913	Z-score 1.96	Prune disabled	FastTree
NDtree	ND_all_1	Assembled contigs from root sample	Z-score 1.96	X 10 x < Y	Neighbor Joining
NDtree	ND_all_2	Assembled contigs from root sample	Z-score 1.96	X 10 x < Y	UPGMA
NDtree	ND_all_3	Assembled contigs from root sample	Pairwise comparison	X 10 x < Y	Neighbor Joining
NDtree	ND_all_4	Assembled contigs from root sample	Z-score 1.64	X 10 x < Y	Neighbor Joining
NDtree	ND_all_5	E. coli NC000913	Z-score 1.96	X 10 x < Y	Neighbor Joining
NDtree	ND_all_6	E. coli NC012759	Z-score 1.96	X 10 x < Y	Neighbor Joining
NDtree	ND_all_7	E. coli NC017641	Z-score 1.96	X 10 x < Y	Neighbor Joining
Realphy	RP_all_1	E. coli NC012759 and E. coli NC000913	Weight ≥ 10	≥95% supports the same nucleotide	RAxML
Realphy	RP_all_2	E. coli NC012759 and E. coli NC000913	Weight ≥ 10	≥ 95% supports the same nucleotide	phyML
Realphy	RP_all_3	E. coli NC012759, E. coli NC000913, E. coli NC017641	Weight ≥ 10	≥ 95% supports the same nucleotide	phyML

ISSN: 1471-2164