Outline of a pairwise partial gene order alignment of two genomes. This figure depicts all required steps to compute a pairwise gene order alignment of two genomes. Step 1 involves the pairwise comparison of all contiguous sequence regions of two species. The alignment matrix is shown for one pairwise comparison of two partially ordered gene sets: A1,2,4,5,6,7,9,10,11,12 and B1,2,3,4a,5a,8,4b,5b,10,11,12. The gene indices express homology relations (e.g. A1 is homologous to B1 and A4 is homologous to B4aand B4b). In this example three alignments were sampled from this pairwise comparison. In step 2, all alignment candidates are sorted in descending order according to their score. Alignments that do not pass a user-defined threshold are discarded. The next step (3) enforces a 1:1 mapping of "matching" vertices. Genes are greedily assigned to one another based on the sorted alignments. The final step (4) merges the two chain graphs into a partial order graph (POG). Matching nodes are "fused" and non-matching nodes are retained as individual nodes.