Table 1.

Epidemiological and genomic data necessary for each method. S stands for sequences, and P for phylogenetic trees. Packages are available for methods in bold. Removal time corresponds to time at which an individual becomes non-infectious, generally the culling time or end of hospitalization, and intrinsic characteristics are either number of individuals present on site or predominant animal species. Didelot et al.’s (2014) [17] method, while not based on a spatial kernel, penalized transmission trees after reconstruction if they did not respect geographical data, hence the parentheses surrounding the geographical data. Hall et al.’s (2015) [18] method could include contact data, but geographical data was used instead.

Family		Method (Name) [Reference]	Start of Exposure	Onset of Infectiousness	Sampling Time	Removal Time	Contact Data	Geographical Data	Intrinsic Characteristics	Phylogenetic Tree or Sequences
Non-phylogenetic		Aldrin et al., 2011 [28]		X		X		X	X	S
		Jombart et al., 2011 (Seqtrack) [16]			X					S
		Ypma et al., 2012 [32]		X		X		X		S
		Jombart et al., 2014 (outbreaker) [24]			X					S
		Worby et al., 2014 [37]			X					S
		Famulare et al. 2015 [38]			X					S
		Worby et al., 2016 (bitrugs) [6]	X		X	X				S
		Campbell et al., 2019 (outbreaker2) [30]			X		X			S
Sequential phylogenetic		Cottam et al., 2008 [2]		X	X	X				P
		Didelot et al., 2014 [17]			X			(X)		P
		Eldholm et al., 2016 [39]			X					P
		Didelot et al., 2017 (Transphylo) [40]			X					P
		Sashittal et al., 2020 (TiTUS) [31]	X		X	X	X			P
Simultaneous phylogenetic	Explicitly phylogenetic	Ypma et al., 2013 [5]		X	X	X		X		S
		Hall et al., 2015 (beastlier) [18]			X	X	(X)	X		S
		De Maio et al., 2016 (SCOTTI) [41]	X		X	X				S
		Klinkenberg et al., 2017 (phybreak) [26]			X					S
	Implicitly phylogenetic	Morelli et al., 2012 [23]		X	X	X		X		S
		Mollentze et al., 2014 [1]			X			X		S
		Lau et al., 2015 [42]		X	X	X		X		S
		Firestone et al., 2020 (BORIS) [29]		X	X	X		X	X	S
		Montazeri et al., 2020 [43]			X					S