Table 1. Percentage of data sets where linkage phase configuration was correctly estimated for five different parental P and Q haplotypes in simulation 1.

Ploidy level	A		B		C
	P	Q	P	Q	P	Q
Autotetraploid ($m=4$)	100	100	99.7	99.8	100	100
	100	100	99.7	99.7	99.9	99.7
	100	100	100	100	99.7	99.8
	100	100	99.9	99.7	99.9	99.9
	100	100	99.9	99.8	100	100
Autohexaploid ($m=6$)	100	100	96.6	97.2	96.1	94.6
	100	100	97.3	97.5	95.8	95.6
	100	100	96.5	96.7	94.7	94.6
	100	100	97.3	97.4	96.1	94.7
	100	100	97.2	97.4	95.2	94.5
Autooctaploid ($m=8$)	100	100	93.6	94.4	93.2	95.7
	100	100	97.6	96.8	92.1	93.9
	100	100	96.8	97.6	90.4	89.2
	100	100	97.7	98.4	90.6	90.0
	100	100	96.9	94.6	88.8	90.6