The complexity of genome evolution poses many exciting challenges to devel- ers of mathematical models and algorithms, who have recourse to a spectrum of algorithmic, statisticalandmathematicaltechniques, rangingfromexact, heur- tic, ?xed-parameter and approximation algorithms for problems based on par- mony models to Monte Carlo Markov Chain algorithms for Bayesian analysis of problems based on probabilistic models. The annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB ComparativeGenomics)is aforumonallaspects andcomponents of this ?eld, rangingfromnew quantitativediscoveriesabout genomestructureand process to theorems on the complexity of computational problems inspired by genome comparison. The informal steering committee for this meeting consists of David Sanko?, Jens Lagergren and Aoife McLysaght. Thisvolumecontainsthepaperspresentedatthe3rdRECOMBComparative Genomicsmeeting, whichwasheldinDublin, Ireland, onSeptember18-20,2005. The ?rst two meetings of this series were held in Minneapolis, USA (2003) and Bertinoro, Italy (2004). This year, 21 papers were submitted, of which the Program Committee - lected 14 for presentation at the meeting and inclusion in this proceedings.Each submission was refereed by at least three members of the Program Committee. Aftercompletionofthereferees'reports, anextensiveWeb-baseddiscussiontook placeformakingdecisions.TheRECOMBComparativeGenomics2005Program Committee consisted of the following 27 members: Vineet Bafna, Anne Be- eron, Mathieu Blanchette, Avril Coghlan, Dannie Durand, Nadia El-Mabrouk, Niklas Eriksen, Aaron Halpern, Rose Hoberman, Daniel Huson, Jens Lagergren, Giuseppe Lancia, Emmanuelle Lerat, Aoife McLysaght, Istvan Miklos, Bernard Moret, PavelPevzner, Ben Raphael, Marie-FranceSagot, David Sanko?, Cathal Seoighe, Beth Shapiro, Igor Sharakhov, Mike Steel, Jens Stoye, Glenn Tesler and Louxin Zhan. We would like to thank the ProgramCommittee members for their dedication and hard wo

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.