Table 2.

Programs and relationship structures

Program [reference]	Relationship structure
	singletons	trios	sib-pairs	larger nuclear families	extended families
FBAT [7, 8]		X	X		decomposed into nuclear families and treated as independent
TRANSMIT [11]		X	X		decomposed into nuclear families and treated as independent
GENEHUNTER TDT [52]		X
PLINK [53]	X	X	X
QTDT [9,10]		X	X
UNPHASED [12]	X	X	X		decomposed into nuclear families and treated as independent
HHRR [29]	X	X
MENDEL [21]	X	X	X	X	X
LAMP [19, 20]	X	X	X	X	small pedigrees only∗
PSEUDOMARKER	X	X	X	X	X

^∗LAMP uses the Lander-Green-algorithm and it can only analyze small extended families in feasible time.