  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.
