NullHap – a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles

Table 3 Computational time comparison

loci	number of haplotypes	observ.	null alleles	time for application
				Arlequin	Phase	HaploIHP	NullHap
2	6	100	no	0.13 s	46 s	0.5 s	0.07 s
2	9	100	no	0.06 s	47 s	0.15 s	0.04 s
3	8	100	no	0.04 s	69 s	0.58 s	0.02 s
2	504	99	no	0.22 s	53 s	-	37 s
2	540	99	no	0.34 s	58 s	-	39 s
5	32	200	yes	-	-	14 s	0.78 s
7	128	200	yes	-	-	145 s	13 s
8	256	200	yes	-	-	450 s	61 s
9	512	200	yes	-	-	1300 s(8 s)	209 s
10	1024	200	yes	-	-	3 h (8 s)	2300 s
11	2048	200	yes	-	-	24 h (10 s)	3 h
15	32768	100	yes	-	-	-	48 h

Computational time for considered applications (HaploIHP in parenthesis with greedy algorithm). Results presented only for applications able to handle the given polymorphism, otherwise '-'.

ISSN: 1471-2105