Abstract
Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions and deletions, far less has been paid to the problem of optimising alignments in the presence of more general rearrangement and copy number variation. Utilising cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new `Cactus' alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.