Rating: - Both theory and practice
This book is an excellent introduction to the basis principles of phylogenetics. The text is especially good for the practicing biologist as it also has a practical component that applies these theoretical concepts. There are downloadable exercises and walk through examples using many of the commonly used phylogentic software. A solid book for the beginner to intermediate practitioner.

The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing