Figure 3.

Local read clustering. The local window of the MSA displayed in Figure 2 is considered (dashed-line rectangle), with colors defined as in Figure 2. Reads that are more similar to each other than to other reads are grouped together which recovers the three original haplotypes A, B, and C of Figure 2 as indicated by the three different colors. Each cluster center sequence is a predicted haplotype (bold, underlined) and the size of its corresponding cluster is an estimate of the frequency of the haplotype (here, 4/f/9, and 2/9, respectively).