求解2种群复制-丢失系统发育问题的分支切割算法
A Branch-and-Cut Algorithm for the 2-Species Duplication-Loss Phylogeny Problem
摘要：
重建一组相关生物体中全基因组进化事件的历史具有巨大的生物学意义。最近引入了一个简化的模型，它只捕获内容修改操作。它允许小的遗传问题被公式化为一个对齐问题。在这项工作中，我们提出了一个分支和切割算法，这个所谓的重复损失对齐问题。我们的方法明显优于现有的基于ILP的方法的几个数量级。我们定义类有效的不等式，并提供算法来有效地分离它们，并证明了NP-困难的重复损失对齐问题。
英文摘要：
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.
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