Table 4.

Maximum likelihood phylogenies of 30 emetic group III outbreak isolates considered to be more topologically similar than would be expected by chance (P < 0.05)^a.

Reference phylogenyb	Query phylogenyb	Corrected P-valuec
AH187_CFSAN_NOdust_all	AH187_CFSAN_NOdust_core	0
AH187_CFSAN_NOdust_all	AH187_LYVE-SET_NOdust_all	0
AH187_CFSAN_NOdust_all	AH187_LYVE-SET_NOdust_core	0.0171
AH187_CFSAN_NOdust_all	AH187_LYVE-SET_YESdust_all	0
AH187_CFSAN_NOdust_all	AH187_LYVE-SET_YESdust_core	0.0171
AH187_CFSAN_NOdust_core	AH187_LYVE-SET_NOdust_all	0
AH187_CFSAN_NOdust_core	AH187_LYVE-SET_NOdust_core	0.0171
AH187_CFSAN_NOdust_core	AH187_LYVE-SET_YESdust_all	0
AH187_CFSAN_NOdust_core	AH187_LYVE-SET_YESdust_core	0.0171
AH187_Freebayes_NOdust_core	AH187_Freebayes_YESdust_core	0.0342
AH187_LYVE-SET_NOdust_all	AH187_LYVE-SET_NOdust_core	0.0171
AH187_LYVE-SET_NOdust_all	AH187_LYVE-SET_YESdust_all	0
AH187_LYVE-SET_NOdust_all	AH187_LYVE-SET_YESdust_core	0.0171
AH187_LYVE-SET_NOdust_core	AH187_LYVE-SET_YESdust_core	0
AH187_LYVE-SET_YESdust_all	AH187_LYVE-SET_YESdust_core	0.0171
AH187_Parsnp_NOdust_core	AH187_Parsnp_YESdust_core	0.0171

^aObtained from pairwise tests of tree topologies using a Z test based on the Kendall-Colijn metric (Kendall and Colijn, 2015; Katz et al., 2017); see Supplementary Table S4 for full table of comparisons.

^bNames of reference and query phylogenies denote reference genome (“AH187” for reference-based pipelines, “NOREF” for reference-free kSNP pipeline), pipeline (“CFSAN,” “Freebayes,” “kSNP,” “LYVE-SET,” “Parsnp,” or “Samtools”), reference genome masking (“NOdust” for an unmasked reference genome, “YESdust” for a dustmasked reference genome, or “NAdust” for reference-free kSNP pipeline, for which dustmasking is not applicable), and SNPs used to construct the phylogeny (“core” for core SNPs, or “all” for core and accessory SNPs), separated by an underscore (“_”).

^cBonferroni-corrected P-values for all tests that were significant at the α = 0.05 level.