Identifying insertion and deletion events. The figure shows an exemplary multiple alignment of orthologous sequence segments in human, chimp and rhesus. The gap containing regions I and D can unambiguously be explained by a single insertion (I) or deletion (D) event in the human lineage since its speciation from the common ancestor with chimp. In contrast, region I* has non-overlapping gaps in chimp and rhesus and therefore requires at least two indel events. These scenarios are always ambiguous. For instance, I* can be explained by an insertion in human and a deletion in chimp, but also by a deletion in chimp and a deletion in rhesus.