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Table 1 Comparison of four algorithms (AWclust, STRUCTURE, BAPS and ipPCA) for inferring the number of primal subpopulations (K).

From: Iterative pruning PCA improves resolution of highly structured populations

Dataset AWclust STRUCTURE BAPS ipPCA
model 1 simulated (3 subpopulations) 3 3 2 3
model 2 simulated (5 subpopulations) 5 6 5 5
model 3 simulated (20 subpopulations, 30 datasets) N/A1 N/D2 113 203
HapMap (4 population labels with 50000 SNPs) 3 3 3 4
bovine (9 population labels with 9329 SNPs) N/A1 10 14 9
Shriver's (14 population labels with 11555 SNPs) N/A1 144 5 12
  1. 1 Not applicable since AWclust gap statistics limits K < 8
  2. 2 Not done owing to the computational constraint
  3. 3 Modal value from 30 simulated datasets
  4. 4 There are two subpopulations with no individuals assigned to them