Fig. 1

Example position-shift map. a A true MSA, which was created by a simulation along the tree in Fig. 2b. b A reconstructed MSA. In the position-shift map (c), each site of each sequence is occupied by the residue’s horizontal position in the reconstructed MSA minus that in the true MSA. d Partitioning the map into position-shift blocks (enclosed by colored boxes). Each of the yellow and green blocks (with shifts 7 and 1, respectively,) was associated with a “shift.” The blue block (with shift 2) and the red one (with shift 14) were paired and associated with a “merge + shift.” The purple one (with shift 2) was judged as accompanying the blue one to result in the “merge.” [NOTE: The rectangles in panel d were drawn manually, based on the output of a prototype script to parse a position-shift map.]