A Lower Bound for the Breakpoint Phylogeny Problem

Breakpoint phylogenies methods have been shown to be an effective way to extract phylogenetic information from gene order data. Currently, the only practical breakpoint phylogeny algorithms for the analysis of large genomes with varied gene content are heuristics with no optimality guarantee. Here we address this shortcoming by describing new bounds for the breakpoint median problem, and for the more complicated breakpoint phylogeny problem. In both cases we employ Lagrangian multipliers and subgradient optimization to tighten the bounds. The experimental results are promising: we achieve lower bounds close to the upper bounds established using breakpoint phylogeny heuristics. 1 Phylogenetic Inference Using Gene Order Data Molecular systematics has long focused on the comparison of DNA or protein sequences which have evolved through the local operations of replacement of one term by another, or the insertion or deletion of one or more terms. With the growing availability of genomic dat...

• Type: Conference
• Year: 2000
• Where: CPM
• Authors: David Bryant
• Keywords: Breakpoint Phylogeny, Combinatorics, CPM 2000, Gene Order Data, Gene Orders