Figure 3

Different representations of the space of possible haplotypes pairs S _i . The left panel (A) shows the list representation commonly used by haplotype software such as Phase v2.1. The lower right panel (C) shows the representation used by Shape-IT. White and black circles indicate the phases between the heterozygous SNPs. On this example we use the same genotype G _i described in Figure 1. For iterations as performed by Phase v2.1 (A), the list requires the exploration of 20 nodes (4 haplotype pairs × 5 SNPs). With the complete tree representation (B) 10 nodes need to be explored, and with the incomplete tree representation as performed by Shape-IT (C), only 7 nodes need to be explored. The difference observed between (B) and (C) results from the pruning strategy which avoids the exploration of the nodes with probability ≤ 0.01.