BackgroundResearch in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems.ResultsWe have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP.ConclusionDendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.

The Colemani integral is a p-adice line integral that can be used to encapsulate several quantities relevant, to a study of the arithmetic of varieties. In this thesis, I describe algorithms for computing Coleman integrals on hyperelliptic curves and discuss some immediate applications. I give algorithms to compute single and iterated integrals on odd models of hyperelliptic curves, as well as the necessary modifications to iplemieit these algorithms for even models. Furthermore, I show how these algorithinis can be used in various situations. The first application is the method of Chabatv to find rational points on curves of genus greater than 1. The second is Mlihyong Kim's recent nonabelian analogue of the Chabauty method for elliptic curves. The last two applications concern p-adic heights on Jacobians of hyperelliptic curves. necessary to formulate a p-adic analogue of the Birch and Swinnerton-Dyer conjecture. I conclude by stating the analogue of the Mazur-Tate-Teitelbaum conjecture iii our setting and presenting supporting data.

The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.

Motivation: Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although promising approaches exist, there are no tools available that biologists could easily and routinely use to compute rooted phylogenetic networks on real datasets containing tens or hundreds of taxa. Biologists are interested in clades, i.e. groups of monophyletic taxa, and these are usually represented by clusters in a rooted phylogenetic tree. The problem of computing an optimal rooted phylogenetic network from a set of clusters, is hard, in general. Indeed, even the problem of just determining whether a given network contains a given cluster is hard. Hence, some researchers have focused on topologically restricted classes of networks, such as galled trees and level-k networks, that are more tractable, but have the practical draw-back that a given set of clusters will usually not possess such a representation.Results: In this article, we argue that galled networks (a generalization of galled trees) provide a good trade-off between level of generality and tractability. Any set of clusters can be represented by some galled network and the question whether a cluster is contained in such a network is easy to solve. Although the computation of an optimal galled network involves successively solving instances of two different NP-complete problems, in practice our algorithm solves this problem exactly on large datasets containing hundreds of taxa and many reticulations in seconds, as illustrated by a dataset containing 279 prokaryotes.Availability: We provide a fast, robust and easy-to-use implementation of this work in version 2.0 of our tree-handling software Dendroscope, freely available from http://www.dendroscope.org.Contact: huson@informatik.uni-tuebingen.de