title: Towards the development of computational tools for evaluating phylogenetic network reconstruction methods.
abstract: We report on a suite of algorithms and techniques that together provide a simulation flow for studying the topological accuracy of methods for reconstructing phylogenetic networks. We implemented those algorithms and techniques and used three phylogenetic reconstruction methods for a case study of our tools. We present the results of our experimental studies in analyzing the relative performance of these methods. Our results indicate that our simulator and our proposed measure of accuracy, the latter an extension of the widely used Robinson-Foulds measure, offer a robust platform for the evaluation of network reconstruction algorithms.
authors.affiliation: Dept. of Computer Sciences, U of Texas, Austin, TX 78712, USA.
authors.forename: Luay
authors.initials: L
authors.lastname: Nakhleh
authors.forename: Jerry
authors.initials: J
authors.lastname: Sun
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
authors.forename: C Randal
authors.initials: CR
authors.lastname: Linder
authors.forename: Bernard M E
authors.initials: BM
authors.lastname: Moret
authors.forename: Anna
authors.initials: A
authors.lastname: Tholse
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D006824:Hybridization, Genetic; D008957:Models, Genetic; D010802:Phylogeny