Identifying orthologs: cycle splitting on the breakpoint graph

Gene rearrangements have successfully been used in phylogenetic reconstruction and comparative genomics but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. This paper approach that problem using gene rearrangement data. Identifying a single gene within each family on the basis of a parsimonious criterion and discarding all others. Steps were taken to remedy this problem by providing an optimization framework derived from the breakpoint graph. The basic structure describing a pair of genomes with no duplicates and equal gene content is the breakpoint graph.