Fig. 2.

Chimeric alignments. We identify three types of chimeric alignment between a query sequence Q and two candidate parents A and B: local, local-X and global-X. A chimeric alignment has two non-overlapping segments of Q, one of which is closer to A than to B by some measure of evolutionary distance while the other is closer to B than to A. In a local chimeric alignment, these two segments can be non-contiguous and may only cover a part of Q. In a local-X alignment, the segments are contiguous with an intervening crossover segment (X) which is identical in Q, A and B. A global-X alignment is a special case of a local-X alignment that covers all of Q, but not necessarily all of A or B.