‘apparent’: a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information

Table 1 Comparison of the ‘apparent’ R package to five currently available tools for parentage analysis, based on main features, ease of use, and available functions

Package/Tool	Main features				Ease of use			Available functions^e
Package/Tool	Marker Type^a	Method of Analysis^b	Required classes^c	OS^d	Parameter-ization	Input	Output	PM	PP	PR	SR	FP	EP	IC	EC
Apparent	Co	GR/GS	none	R	Easy	Easy	Easy	X	X	X				X
hsphase (pogc)	Co	GR/GS	none	R	Easy	Easy	Complex			X	X
MasterBayes (MCMCped)	Co/Do	BA/ML	Pa/Off	R	Complex	Easy	Easy	X	X	X		X		X	X
ParentOffspring	Co	GR/GS	Mo/Fa/Off	R	Easy	Easy	Easy		X
Solomon	Co	BA	Pa/Off	R	Moderate	Easy	Moderate	X	X				X	X	X
Cervus	Co/Do	ML	Pa/Off	W	Moderate	Easy	Moderate	X	X				X	X	X

^aCo = Co-dominant, Do = Dominant
^bBA = Bayesian approach; GR = Genetic relatedness, GS = Genetic similarity, ML = Maximum likelihood
^cnone = no a priori information required for individuals, Pa/Off = each individual must be classified as either a Parent or an Offspring [2 classes], Fa/Mo/Off = each individual must be uniquely classified as a potential Mother, Father, or Offspring [3 classes]
^dOperational System. R = R package (OS independent), W = Windows
^eFollowing the typology developed by Jones et al. (2010): PM = Paternity/maternity analysis, PP = Parent pair allocation, PR = Parental reconstruction analysis, SR = Sib-ship Reconstruction, FP = Full probability analysis, EP = Ability to calculate exclusion probabilities, IC = Ability to assign statistical confidence to individual parent-offspring pairs, EC = Ability to assess experiment-wide statistical confidence of parent-offspring assignments

ISSN: 1471-2105