Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation

Tandy Warnow

doi:10.1017/9781316882313

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Computational Phylogenetics

Computational Phylogenetics

An Introduction to Designing Methods for Phylogeny Estimation

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Tandy Warnow, University of Illinois, Urbana-Champaign

Publisher: Cambridge University Press
Online publication date: October 2017
Print publication year: 2017
Online ISBN: 9781316882313
DOI: https://doi.org/10.1017/9781316882313

Subjects: Computer Science, Computational Biology and Bioinformatics, Applied Probability and Stochastic Networks, Statistics and Probability

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Computational Phylogenetics
Tandy Warnow
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Book DOI: https://doi.org/10.1017/9781316882313
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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.

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Computational Phylogenetics

An Introduction to Designing Methods for Phylogeny Estimation

This book has been cited by the following publications. This list is generated based on data provided by CrossRef.

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Contents

Frontmatter
pp i-iv

Dedication
pp v-vi

Contents
pp vii-xii

Preface
pp xiii-xvi

Glossary
pp xvii-xvii

Notation
pp xviii-xviii

PART I - BASIC TECHNIQUES
pp 1-2

1 - Brief Introduction to Phylogenetic Estimation
pp 3-28

2 - Trees
pp 29-50

3 - Constructing Trees from True Subtrees
pp 51-60

4 - Constructing Trees from Qualitative Characters
pp 61-82

5 - Distance-based Tree Estimation Methods
pp 83-108

6 - Consensus and Agreement Trees
pp 109-120

7 - Supertrees
pp 121-142

PART II - MOLECULAR PHYLOGENETICS
pp 143-144

8 - Statistical Gene Tree Estimation Methods
pp 145-177

9 - Multiple Sequence Alignment
pp 178-233

10 - Phylogenomics: Constructing Species Phylogenies from Multi-Locus Data
pp 234-273

11 - Designing Methods for Large-Scale Phylogeny Estimation
pp 274-298

Appendix A - Primer on Biological Data and Evolution
pp 299-303

Appendix B - Algorithm Design and Analysis
pp 304-326

Appendix C - Guidelines forWriting Papers About Computational Methods
pp 327-330

Appendix D - Projects
pp 331-338

References
pp 339-375

Index
pp 376-379

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An Introduction to Designing Methods for Phylogeny Estimation

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