Table 1.

Influence of the clusthaplo parameters on the average number of ancestor alleles and the number of clustering changes, defined by the change of at least one haplotype in the clustering result from locus to locus (373 clustering points in total)

Parameters	Default
w 1	Exp.	Exp.	Exp.	Exp.	Exp.	Exp.	Exp.	Laplace	Gauss	Unif.	Exp.	Laplace	Gauss
w 2	Unif.	Unif.	Unif.	Unif.	Unif.	Unif.	Unif.	Unif.	Unif.	Unif.	1	1	1
Window length	20	15	10	5	1	20	20	20	20	20	20	20	20
Na.replace	Truea	True	True	True	True	Nab	Falsec	True	True	True	True	True	True
Li and Jiang’s score, threshold by equilibrium sampling
Nb alleles	4.25	4.89	5.52	5.91	3.70	4.62	4.68	4.50	4.43	4.15	4.66	4.70	4.68
Nb changes	138	155	135	143	175	131	133	143	146	144	163	154	162
Extended Li and Jiang’s score, threshold by equilibrium sampling
Nb alleles	4.14	4.52	4.22	4.55	4.17	4.50	4.51	4.40	4.33	4.04	4.61	4.64	4.64
Nb changes	138	168	177	220	198	127	130	148	143	140	159	152	154

^aComparison of alleles involving missing data gives always a true result

^bComparison of alleles involving missing data gives a non-assigned result

^cComparison of alleles involving missing data gives a false result