A fast method for large-scale multichromosomal breakpoint median problems.

We provide a computationally realistic mathematical framework for the NP-hard problem of the multichromosomal breakpoint median for linear genomes that can be used in constructing phylogenies. A novel approach is provided that can handle signed, unsigned, and partially signed cases of the multichromosomal breakpoint median problem. Our method provides an avenue for incorporating biological assumptions (whenever available) such as the number of chromosomes in the ancestor, and thus it can be tailored to obtain a more biologically relevant picture of the median. We demonstrate the usefulness of our method by performing an empirical study on both simulated and real data with a comparison to other methods.