The Phylogenetic Handbook is a broad, hands on guide to theory and
practice of nucleotide and protein phylogenetic analysis. This
second edition includes six new chapters, covering topics such as
Bayesian inference, tree topology testing and 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 and
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 and
phylogeny software, including BLAST, FastA, Clustal, T-coffee,
Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL,
ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC,
SplitsTree, and RDP. 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.
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