An example of a hypothetical HSP layout between two genomes A and B as produced during the GBDP alignment phase. Subsequences that are part of an HSP in either A or B are labeled with small letters a-g. A special case is represented by segment “c” where both HSP 2 and HSP 3 are overlapping. GBDP’s algorithms are programmed to handle these distinctly, i.e., (i) by simply completely omitting the smaller HSP 3 (“greedy” algorithm), (ii) by omitting only segment “c”, i.e. trimming HSP 3 (“greedy-with-trimming” algorithm), or (iii) by merging information from both HSPs regarding the overlapping segment (“coverage” algorithm). (Figure redrawn from ).