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 performanc...

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix CHAPTER 1. General Introduction . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Computational Phylogenetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1.1 The Perfect Phylogeny Problem . . . . . . . . . . . . . . . . . . . . . . . 2 1.1.2 The Tree Compatibility Problem . . . . . . . . . . ....

We prove that Nakhleh’s latest ‘metric’ for phylogenetic networks is a metric on the classes of tree-child phylogenetic networks, of semi-binary time consistent tree-sibling phylogenetic networks, and of multi-labeled phylogenetic trees.We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks ava...

Answering a problem posed by Nakhleh, we prove that counting the number of phylogenetic trees inferred by a (binary) phylogenetic network is #P-complete. An immediate consequence of this result is that counting the number of phylogenetic trees commonly inferred by two (binary) phylogenetic networks is also #P-complete.

There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the underlying data, phylogenetic trees are in general not completely resolved and, thus, those methods can often not be applied to biological data. In this work...

colibacillosis caused by avian pathogenic escherichia coli (apec) is an economic threat to the poultry industry throughout the world. some of the virulence genes may enhance the ability of e. coli isolates to grow in the tissues of broilers. the apec strains are assigned to a few distinct phylogenetic groups. the purpose of the present study was to detect the virulence genes and phylogenetic gr...

Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecular datasets. Here, we compare several models for combining different genes for ...