Table 1.

The transmission network reconstruction tools evaluated in this study, detailing the epidemiological features and input data type for each tested approach

Transmission reconstruction model	Input data type	Prior generation time distribution	Prior mutation rate estimate	Can use spatial data	Can use contact-tracing data	Within-host evolution	Unsampled hosts	Estimates infection times
BEASTLIER	SNP alignment	Yes	Yes	Yes	No	Yes	No	Yes
Outbreaker2	SNP alignment	Yes	Yes	No	Yes	Yes	Yes	Yes
Phybreak	SNP alignment	Yes	Yes	No	No	Yes	No	Yes
SCOTTI	SNP alignment	No	Yes	No	No	Yes	Yes	No
seqTrack	SNP distance matrix	No	Yes	Yes	No	No	No	No
TransPhylo	Timed phylogenetic tree(s)	Yes	Yes	No	No	Yes	Yes	Yes