Fig. 4

Example indel history and resulting alignments. a An example indel history in terms of the bra-vectors of sequence states and indel operators. b The graphical illustration of the history using basic sequence states. Each sequence state in panel a is horizontally aligned with its graphical representation in panel b. c The resulting MSA among the sequence states that the indel history went through. d The resulting PWA between the initial and final sequences. In both c and d, the bold italicized characters in the leftmost column are the suffixes indicating the sequence states in panel a. In panels b, c, and d, the number in each site (cell) represents its ancestry, but not necessarily its position along the sequence. The ‘A’ in the final sequence abbreviates 10. The same shading scheme as in Fig. 1 is used. The figure was adapted from Fig. 1 of [32]