The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing

Basic concepts of molecular evolution / Anne-Mieke Vandamme

Sequence databases and database searching. Theory / Guy Bottu ; Practice / Marc Van Ranst and Philippe Lemey

Multiple sequence alignment / Des Higgins and Philippe Lemey

Genetic distances and nucleotide substitution models. Theory / Korbinian Strimmer and Arndt von Haeseler ; Practice / Marco Salemi

Phylogenetic inference based on distance methods. Theory / Yves van de Peer ; Practice / Marco Salemi

Phylogenetic inference using maximum likelihood methods / Heiko A. Schmidt and Arndt von Haeseler

Bayesian phylogenetic analysis using MrBayes / Fredrik Ronquist, Paul van der Mark, and John P. Huelsenbeck

Phylogeny inference based on parsimony and other methods using PAUP / David L. Swofford and Jack Sullivan

Phylogenetic analysis using protein sequences. Theory / Fred R. Opperdoes ; Practice / Fred R. Opperdoes and Philippe Lemey

Selecting models of evolution / David Posada

Molecular clock analysis / Philippe Lemey and David Posada

Testing tree topologies / Heiko A. Schmidt

Natural selection and adaptation of molecular sequences / Oliver G. Pybus and Beth Shapiro

Estimating selection pressures on alignments of coding sequences / Sergei L. Kosakovsky Pond, Art F.Y. Poon, and Simon D.W. Frost

Introduction to recombination detection / Philippe Lemey and David Posada

Detecting and characterizing individual recombination events / Mika Salminen and Darren Martin

The coalescent : population genetic inference using genealogies / Allen Rodrigo

Bayesian evolutionary analysis by sampling trees / Alexei J. Drummond and Andrew Rambaut

LAMARC : estimating population genetic parameters from molecular data / Mary K. Kuhner

Assessing substitution saturation with DAMBE. Theory / Xuhua Xia ; Practice / Xuhua Xia and Philippe Lemey

Split networks. A tool for exploring complex evolutionary relationships in molecular data / Vincent Moulton and Katharina T. Huber.