Table 1.

Accuracies of ancestry estimates obtained by the compared methods on the HapMap admixtures

Method	YRI-CEU	CEU-JPT	JPT-CHB
SABER	89.4	85.2	68.2
HAPAA	93.7	88.2	72.0
LAMP	94.8	93.0	65.8
LAMP-EM	97.8	94.8	74.8
WINPOP	98.0	95.9	82.8
WINPOP-EM	97.7	94.7	74.8
Upper bound	99.9	99.6	91.9

LAMP-EM (WINPOP-EM) uses LAMP (WINPOP) solution as an initialization for an EM algorithm that optimizes an HMM similar to the model proposed in STRUCTURE (see Section 2.4 for details).