Direct maximum parsimony phylogeny reconstruction from genotype data

BMC Bioinformatics

Table 1 Positive and negative errors for indirect phylogeny inference with varying mutation rate

SNPs	n _H	Method	θ = 0.20	0.25	0.30	0.35	0.40	0.45	0.50	0.55	0.60
5	30	fastPHASE positive errors	2	8	8	13	7	15	14	8	14
5	30	fastPHASE negative errors	1	8	1	5	11	16	19	19	26
5	30	haplotyper positive errors	1	10	2	10	3	6	12	5	12
5	30	haplotyper negative errors	1	8	2	5	11	17	22	21	26
10	30	fastPHASE positive errors	7	12	27	38	28	38	38	27	42
10	30	fastPHASE negative errors	10	12	9	11	24	29	24	23	26
10	30	haplotyper positive errors	7	14	15	23	28	24	37	41	40
10	30	haplotyper negative errors	11	11	12	11	21	31	20	18	25
5	60	fastPHASE positive errors	6	7	7	15	16	13	16	11	14
5	60	fastPHASE negative errors	2	3	3	7	7	7	12	12	21
5	60	haplotyper positive errors	5	3	3	9	7	8	7	7	6
5	60	haplotyper negative errors	2	2	3	9	10	9	14	15	24
10	60	fastPHASE positive errors	24	25	25	29	28	32	43	54	41
10	60	fastPHASE negative errors	4	11	20	14	12	17	27	23	36
10	60	haplotyper positive errors	11	13	14	13	22	25	27	42	34
10	60	haplotyper negative errors	7	12	24	18	11	21	28	22	29

The table separates the phylogenetic errors from the experiments of Figure 2 into positive and negative errors for indirect phylogeny inference using fastPHASE and haplotyper.

ISSN: 1471-2105