Figure 1.
Ancestor alignments. Examples of different forms of sequence alignment. (A) A pairwise alignment of two sequences. (B) The same pairwise alignment as in A, but with the addition of an ancestor sequence that resolves the ambiguous questions posed in A. (C) A multiple sequence alignment containing the sequences in A and B. By eye, it is possible to resolve the questions in A with some confidence, although the multiple sequence alignment provides no explicit answers and contains nested indel events. (D) A multiple sequence ancestor alignment, which contains explicit ancestor sequences for every node in the phylogeny. The inference of such alignments is the task of Ortheus.
