Table 1.

Overview of recent inference methods for the bi-allelic Wright–Fisher model

Reference	Data	Mut	Mig	Sel	Approach	Availability
Markov chain theory
Mathieson and McVean (2013)a	T				Normal	-
Gompert (2015)a	T				Beta	spatpg
Diffusion approximation
Bollback et al. (2008)	T				Finite-difference	-
Gutenkunst et al. (2009)	S				Finite-difference	ai
Lukić and Hey (2012)	S				Spectral decomposition	MultiPop
Malaspinas et al. (2012)	T				Numerical approximation	upon request
Gautier and Vitalis (2013)	S				Spectral decomposition	KimTree
Steinrücken et al. (2014)	T				Spectral decomposition	spectralHMM
Vitalis et al. (2014)	S				Stationary DAF	SelEstim
Živković et al. (2015)	S				Spectral decomposition	upon request
Ferrer-Admetlla et al. (2016)	T				Numerical approximation	ApproxWF
Moment-based approximations
Sirén et al. (2011)	S				Beta	-
Pickrell and Pritchard (2012)	S				Normal	TreeMix
Lacerda and Seoighe (2014)	T				Normal	upon request
Hui and Burt (2015)	T				Beta	NB
Tataru et al. (2015)	S				Beta with spikes	SpikeyTree
Terhorst et al. (2015)	T				Normal	EandR-timeseries

The table indicates what type of data the method uses (Data): time series data from one population (T) or single time-point data from multiple populations (S); if the method models new mutations (Mut), migration (Mig) or selection (Sel); which type of approach is used for calculating the DAF (Approach); and whether the method is publicly available (Availability). All methods model genetic drift.

^a analyze jointly time series data from multiple populations. The table covers only the more recent inference methods.