Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach

TL;DR

This paper introduces an integer programming approach to solve the persistent phylogeny problem, extending perfect phylogeny models, and demonstrates its efficiency and the conditions under which persistent phylogenies are galled trees.

Contribution

It develops a novel integer programming method for persistent phylogeny and empirically evaluates its performance and the relationship with galled trees.

Findings

Integer programming efficiently identifies large persistent phylogenies.

Persistent phylogenies often correspond to galled trees within certain parameters.

The approach outperforms previous methods in size scalability.

Abstract

The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely investigated in recent years. In this paper, we explore two alternative approaches to the persistent-phylogeny problem that grow out of our previous work on perfect phylogeny, and on galled trees. We develop an integer programming solution to the Persistent-Phylogeny Problem; empirically explore its efficiency; and empirically explore the utility of using fast algorithms that recognize galled trees, to recognize persistent phylogeny. The empirical results identify parameter ranges where persistent phylogeny are galled trees with high frequency, and show that the integer programming approach can efficiently identify persistent phylogeny of much larger size than has been previously reported.