Table 1 Simulation parameter values and mean of inferred parameter values across 5 simulation and inference replicates

Case Study 1 – Salmonella enterica Bareilly

Input

Inferred

Close ref

Far ref

Number of SNPs

100

98.6 (1.4)

38,384 (mutations)

154 (3) variable sites

RF distance

-

33 (1)

33 (1)

Outbreak clade monophyletic

-

5/5

5/5

Base frequencies

A

0.238787

0.24 (0.03)

0.25 (0.0)

C

0.261361

0.26 (0.03)

0.25 (0.0)

G

0.261132

0.24 (0.03)

0.25 (0.0)

T

0.238720

0.27 (0.03)

0.24 (0.0005)

GTR rate Matrix

ac

0.4

0.1 (0.7)

1.5 (0.6)

ag

T 3.0

91 (160)

5.4 (2.0)

at

0.5

21 (39)

1.0 (0.6)

cg

0.1

0.1 (0.2)

1.5 (0.7)

ct

4.4

66 (112)

5.3 (1.9)

gt

1

1.0 (0.0)

1.0 (0.0)

Coverage

20

17.04 (0)

15.45 (0)

Case Study 2 – Listeria monocytogenes

Input

Inferred

Number of SNPs

500

494.8 (1.6)

RF distance

-

0.0 (0)

Base frequencies

A

0.311521

0.30 (0.01)

C

0.190709

0.20 (0.01)

G

0.189125

0.20 (0.007)

T

0.308645

0.29 (0.007)

GTR rate Matrix

ac

1.2070

1.1 (0.1)

ag

5.9306

5.3 (0.8)

at

1.7425

1.8 (0.2)

cg

0.4610

0.3 (0.2)

ct

5.1238

5.1 (0.7)

gt

1

1.0 (0.0)

Coverage

40

37.49 (0)

Difference from INDELible gap distribution

0

0.0 (0)