## The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis TestingThe 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. |

### What people are saying - Write a review

This textbook comes with online data sets to be used with the tutorials in each chapter. The data sets can be extremely helpful because different programs take different input formats (FASTA, NEXUS, extended-NEXUS, etc) and it can be frustrating for new users to figure out the format(s) that each program will accept. The authors of each chapter were carefully chosen for their expertise in the subject area and many of the chapters were written by the actual authors of the software packages being described. Many of the chapters cover very sophisticated analyses that are beyond the needs of most evolutionary biologists, but there are also chapters covering the more simple and straightforward methods that EVERY biology student and researcher should become familiar with.

### Contents

33 | |

Practice | 55 |

Multiple sequence alignment | 68 |

Practice | 100 |

Genetic distances and nucleotide substitution models | 111 |

Practice | 126 |

Phylogenetic inference based on distance methods | 142 |

Practice | 161 |

Natural selection and adaptation of molecular sequences | 407 |

Estimating selection pressures on alignments of coding sequences | 419 |

Practice | 452 |

Recombination | 493 |

Detecting and characterizing individual recombination events | 519 |

Practice | 532 |

population genetic inference using genealogies | 551 |

Bayesian evolutionary analysis by sampling trees | 564 |

Phylogenetic inference using maximum likelihood methods | 181 |

Bayesian phylogenetic analysis using MRBAYES | 210 |

Practice | 237 |

Phylogeny inference based on parsimony and other methods | 267 |

Practice | 289 |

Phylogenetic analysis using protein sequences | 313 |

Selecting models of evolution | 345 |

Practice | 355 |

H Molecular clock analysis | 362 |

Practice | 373 |

Testing tree topologies | 381 |

Practice | 397 |