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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.
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