  The reconstruction of the history of evolutionary genome-wide events among a
set of related organisms is of great biological interest. A simplified model
that captures only content modifying operations was introduced recently. It
allows the small phylogeny problem to be formulated as an alignment problem. In
this work we present a branch-and-cut algorithm for this so-called
duplication-loss alignment problem. Our method clearly outperforms the existing
ILP based method by several orders of magnitude. We define classes of valid
inequalities and provide algorithms to separate them efficiently and prove the
NP-hardness of the duplication-loss alignment problem.
