Appendix 5—table 12. Parameters and results for scenarios with transmission rate = 1.2 and different thresholds on the minimum tree size.

mts: minimum tree size, λ: transmission rate, ε: sampling rate, R0 = λ/(ε+σ), σ: death rate, ψ: rate of progression to infectiousness, π: molecular clock rate in expected nucleotide changes per site per year, 95% SNP threshold: the minimum SNP threshold for which at least 95% of samples are clustered in at least 95% of simulations, 100% SNP threshold: the minimum SNP threshold for which 100% of samples are clustered in at least 95% of simulations, 95% CI TBL: the confidence interval for the overall TBL distribution, Mean TBL: average terminal branch length for the overall TBL distribution in SNPs, Mean TBL: average of the overall TBL distribution.

Scenario	λ	ε	R0	σ	ψ	π	95% SNP threshold	100% SNP threshold	95% CI TBL	Mean TBL
mts = 25	1.2	1	1.2	0	1	8 × 10–8	4	14	0–2	0.34
mts = 50	1.2	1	1.2	0	1	8 × 10–8	4	15	0–2	0.34
mts = 100	1.2	1	1.2	0	1	8 × 10–8	4	16	0–2	0.34
mts = 200	1.2	1	1.2	0	1	8 × 10–8	3	17	0–2	0.34