Research Catalog

Title

Analysis of phylogenetics and evolution with R / Emmanuel Paradis.

Author

Paradis, Emmanuel.

Publication

New York : Springer, ©2006.

Items in the Library & Off-site

Details

Description

xii, 211 pages : illustrations; 24 cm

Summary

"The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completely updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters."--Publisher's website.

Series Statement

Use R!

Uniform Title

Use R!

Subject

• Cladistic analysis
• Phylogeny > Methodology
• R (Computer program language)
• Biology > classification
• Biology > methods
• Electronic Data Processing
• phylogeny
• evolution
• data analysis
• computer software
• Cladistic analysis
• R Programm
• Phylogenetik
• Evolution
• Datenanalyse
• Filogènia
• R (Llenguatge de programació)
• Analyse cladistique
• Phylogénie > Méthodologie
• R (logiciel)

Bibliography (note)

• Includes bibliographical references (p. [199]-208) and index.

Contents

1.1 Strategic Considerations 1 -- 1.2 Notations 4 -- 1.3 Preparing the Computer 5 -- 1.3.1 Installations 5 -- 1.3.2 Configurations 7 -- 2 First Steps in R for Phylogeneticists 9 -- 2.1 The Command Line Interface 9 -- 2.2 The Data Structures 11 -- 2.2.1 Vector 11 -- 2.2.2 Factor 14 -- 2.2.3 Matrix 15 -- 2.2.4 Data Frame 16 -- 2.2.5 List 17 -- 2.3 The Help System 18 -- 2.4 Creating Graphics 19 -- 2.5 Saving and Restoring R Data 20 -- 2.6 Using R Functions 20 -- 2.7 Repeating Commands 21 -- 2.7.1 Loops 21 -- 2.7.2 Apply-Like Functions 22 -- 3 Phylogenetic Data in R 25 -- 3.1 Phylogenetic Data as R Objects 25 -- 3.1.1 The Class "phylo" (ape) 26 -- 3.1.2 The Class "phylog" (ade4) 27 -- 3.1.3 The Class "matching" (ape) 27 -- 3.1.4 The Class "treeshape" (apTreeshape) 28 -- 3.2 Reading Phylogenetic Data 28 -- 3.2.1 Phylogenies 28 -- 3.2.2 Reading Internet Tree Databases 30 -- 3.2.3 Molecular Sequences 30 -- 3.3 Writing Data 33 -- 3.4 Manipulating Data 35 -- 3.4.1 Basic Tree Manipulation 35 -- 3.4.2 Rooted Versus Unrooted Trees 36 -- 3.4.3 Dichotomous Versus Multichotomous Trees 37 -- 3.4.4 Summarizing and Comparing Trees 38 -- 3.4.5 Converting Objects 39 -- 3.4.6 Manipulating DNA Data 40 -- 3.5 Generating Random Trees 44 -- 3.6.1 Sylvia Warblers 46 -- 3.6.2 Phylogeny of the Felidae 50 -- 3.6.3 Snake Venom Proteome 52 -- 3.6.4 Mammalian Mitochondrial Genomes 55 -- 3.6.5 Butterfly DNA Barcodes 62 -- 4 Plotting Phylogenies 65 -- 4.1 Simple Tree Drawing 65 -- 4.1.1 Annotating Trees 71 -- 4.1.2 Showing Clades 80 -- 4.2 Combining Plots 83 -- 4.3 Large Phylogenies 89 -- 5 Phylogeny Estimation 95 -- 5.1 Distance Methods 96 -- 5.1.1 Calculating Distances 96 -- 5.1.2 Simple Clustering and UPGMA 99 -- 5.1.3 Neighbor-Joining 100 -- 5.2 Maximum Likelihood Methods 100 -- 5.2.1 Substitution Models: A Primer 101 -- 5.2.2 Estimation with Molecular Sequences 106 -- 5.2.3 Finding the Maximum Likelihood Tree 110 -- 5.2.4 DNA Mining with PHYML 111 -- 5.3 Bootstrap Methods and Distances Between Trees 112 -- 5.3.1 Resampling Phylogenetic Data 113 -- 5.3.2 Bipartitions and Computing Bootstrap Values 115 -- 5.3.3 Distances Between Trees 118 -- 5.3.4 Consensus Trees 118 -- 5.4 Molecular Dating 119 -- 5.5.1 Sylvia Warblers 121 -- 5.5.2 Phylogeny of the Felidae 125 -- 5.5.3 Butterfly DNA Barcodes 129 -- 6 Analysis of Macroevolution with Phylogenies 133 -- 6.1 Phylogenetic Comparative Methods 133 -- 6.1.1 Phylogenetically Independent Contrasts 135 -- 6.1.2 Phylogenetic Autoregression 138 -- 6.1.3 Autocorrelative Models 139 -- 6.1.4 Multivariate Decomposition 142 -- 6.1.5 Generalized Least Squares 144 -- 6.1.6 Generalized Estimating Equations 147 -- 6.1.7 Mixed Models and Variance Partitioning 149 -- 6.1.8 The Ornstein-Uhlenbeck Model 151 -- 6.2 Estimating Ancestral Characters 154 -- 6.2.1 Continuous Characters 155 -- 6.2.2 Discrete Characters 156 -- 6.3 Analysis of Diversification 160 -- 6.3.1 Graphical Methods 161 -- 6.3.2 Birth-Death Models 163 -- 6.3.3 Survival Models 167 -- 6.3.4 Goodness-of-Fit Tests 169 -- 6.3.5 Tree Shape and Indices of Diversification 170 -- 6.5.1 Sylvia Warblers 173 -- 6.5.2 Phylogeny of the Felidae 176 -- 7 Developing and Implementing Phylogenetic Methods in R 183 -- 7.1 Features of R 183 -- 7.1.1 Object-Orientation 183 -- 7.1.2 Variable Definition and Scope 185 -- 7.1.3 How R Works 186 -- 7.2 Writing Functions in R 187 -- 7.3 Interfacing R with Other Languages 189 -- 7.3.1 Simple Interfaces 189 -- 7.3.2 Complex Interfaces 190 -- 7.4 Writing R Packages 192 -- 7.4.1 A Minimalist Package 192 -- 7.4.2 The Documentation System 193 -- 7.5 Performance Issues and Strategies 193.

ISBN

• 0387329145
• 9780387329147
• 9780387351001
• 0387351000

LCCN

• 2006923823
• 9780387329147

OCLC

• ocm71298831
• 71298831
• SCSB-1405878

Owning Institutions

Princeton University Library