Book on Phylogenetic Networks

This is the official website (www.phylogenetic-networks.org) for our book entitled "Phylogenetic Networks" by Daniel H. Huson and Regula Rupp, to be published by Cambridge University Press in 2010.

Although many biologists believe that reticulate events such as hybridization, horizontal gene transfer, recombination and reassortment play an important role in evolution, most published studies use trees to represent the evolutionary history for the set of species studied. One reason for this is the lack of robust and accepted methods for inferring non-tree histories or phylogenetic networks. A lot of work has been done in recent years to address this problem.  Our work in this area was originally focused on developing methods for inferring unrooted phylogenetic networks and our computer program, SplitsTree, is currently the most widely-used software for the construction of phylogenetic networks. More recently, we have focused on developing methods for rooted phylogenetic networks, which we make available via our popular Dendroscope tree- and network drawing program.

Phylogenetic networks were one of the main topics of the four month research programme on Phylogenetics held at the Newton Institute of Cambridge University in 2007. There we formed the impression that the field of phylogenetic networks had advanced to a point where there was enough material to warrant a book that gives an introduction to the field and attempts to present the different questions and approaches in a unified manner. Our goal was to write a book that covers the field in a style that is accessible to bioinformatics, biologists that are interested in methods and algorithms and computer scientists that are interested in evolution. This book is the ideal companion for our SplitsTree4 and Dendroscope2 programs.

Table of contents:

Part I Introduction
1.    Basics
2.    Sequence alignment
3.    Phylogenetic trees
4.    Phylogenetic networks
Part II Theory
5.    Clusters and rooted phylogenetic network
6.    Splits and unrooted phylogenetic networks
Part III Algorithms and Applications
7.    Phylogenetic networks from clusters
8.    Phylogenetic networks from splits
9.    Phylogenetic networks from sequences
10.    Phylogenetic networks from distances
11.    Phylogenetic networks from trees
12.    Phylogenetic networks from triplets or quartets
13.    Drawing phylogenetic networks
14.    Software
Glossary

Approx. 330 pages, 180 figures, 70 exercises

Datasets, links and errata will be made available on this website.