The Phylogenetic Handbook is a broad hands on guide to theory & practice of nucleotide & protein phylogenetic analysis. This second edition
Includes:: six new chapters covering topics such as Bayesian inference tree topology testing & the impact of recombination on phylogenies as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition with more extensive discussions on recombination analysis detecting molecular adaptation & genealogy-based population genetics. Many chapters include elaborate practical sections which have been updated to introduce the reader to the most recent versions of sequence analysis & phylogeny software including BLAST Fast A Clustal T-coffee Muscle DAMBE Tree-puzzle Phylip MEGA PAUP* IQPNNI CONSEL Model Test Prottest PAML HYPHY Mr Bayes BEAST LAMARC Splits Tree & RDP. Many analysis tools are described by their original authors resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate & graduate students.