Marco Salemi is Assistant Professor at the Department of Pathology, Immunology and Laboratory Medicine of the University of Florida School of Medicine, Gainesville, USA. His research focuses on molecular evolution of viruses by integrating molecular biology and computational approaches. He has been an EMBO Fellow and a Marie-Curie Fellow in the Evolutionary Biology Group at the Department of Zoology, University of Oxford. Philippe Lemey is a FWO postdoctoral researcher at the Rega Institute, Katholieke Universiteit Leuven, Belgium, where he completed his Ph.D. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including Blast, FastA, Clustal, T-coffee, Muscle, Dambe, Tree-Puzzle, Phylip, Mega4, Paup*, Iqpnni, Consel, ModelTest, ProtTest, Paml, HyPhy, MrBayes, Beast, Lamarc, SplitsTree, and Rdp3.
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The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. This second edition includes seven new chapters, covering topics such as Bayesian inference, tree topology testing, and the impact of recombination on phylogenies. The Phylogenetic Handbook provides a comprehensive introduction to theory and practice of nucleotide and protein phylogenetic analysis.