A thorough explanation of both fundamental and sophisticated concepts in phylogeny estimate with a focus on computational and statistical difficulties. Since no prior knowledge of biology or computer science is assumed and few mathematical formulas are used, the material will be understandable to students of various academic fields, including biology, computer science, statistics, and applied mathematics. After a thorough presentation of the mathematical and statistical underpinnings of phylogeny estimation, more complex information is covered. This contains in-depth chapters on building methods for large-scale phylogeny estimate, supertree approaches, multiple sequence alignment techniques, and multi-locus phylogeny estimation. The author discusses the effectiveness of approaches for estimating trees in practise as well as important analytical tools to demonstrate theoretical properties concerning methods. A comprehensive account of both basic and advanced material in phylogeny estimation, focusing on computational and statistical issues. No background in biology or computer science is assumed, and there is minimal use of mathematical formulas, meaning that students from many disciplines, including biology, computer science, statistics, and applied mathematics, will find the text accessible. The mathematical and statistical foundations of phylogeny estimation are presented rigorously, following which more advanced material is covered. This includes substantial chapters on multi-locus phylogeny estimation, supertree methods, multiple sequence alignment techniques, and designing methods for large-scale phylogeny estimation. The author provides key analytical techniques to prove theoretical properties about methods, as well as addressing performance in practice for methods for estimating trees. Research problems requiring novel computational methods are also presented, so that graduate students and researchers from varying disciplines will be able to enter the broad and exciting field of computational phylogenetics Title Contents Preface Glossary Notation Part I. Basic Techniques 1. Brief Introduction to Phylogenetic Estimation 2. Trees 3. Constructing Trees from True Subtrees 4. Constructing Trees from Qualitative Characters 5. Distance-based Tree Estimation Methods 6. Consensus and Agreement Trees 7. Supertrees Part II. Molecular Phylogenetics 8. Statistical Gene Tree Estimation Methods 9. Multiple Sequence Alignment 10. Phylogenomics: Constructing Species Phylogenies from Multi-Locus Data 11. Designing Methods for Large-Scale Phylogeny Estimation Appendix A. Primer on Biological Data and Evolution Appendix B. Algorithm Design and Analysis Appendix C. Guidelines for Writing Papers About Computational Methods Appendix D. Projects References Index Errata Tandy Warnow, University Of Illinois, Urbana-champaign. Includes Bibliographical References (pages 339-375) And Index.
