1. 1
    Published 1983
    Serial
  2. 2
  3. 3
    by Paradis, Emmanuel
    Published 2012
    Table of Contents ...Analysis of Phylogenetics andEvolution with R; Preface to the Second Edition; Preface to the First Edition; Contents; 1 Introduction; 1.1 Strategic Considerations; Interactivity; Programmability; Evolvability; 1.2 Notations; 1.3 Preparing the Computer; 1.3.1 Installations; 1.3.2 Configurations; 1.4 Other Readings; 2 First Steps in R for Phylogeneticists; 2.1 The Command Line Interface; 2.2 The Help System; 2.3 The Data Structures; 2.3.1 Vector; 2.3.2 Factor; 2.3.3 Matrix; 2.3.4 Data Frame; 2.3.5 List; 2.4 Creating Graphics; 2.5 Saving and Restoring R Data; 2.6 Using R Functions; 2.7 Repeating Commands2.7.1 Loops; 2.7.2 Apply-Like Functions; 2.8 Exercises; 3 Phylogenetic Data in R; 3.1 Phylogenetic Data as R Objects; 3.1.1 Trees; The Class "phylo" (ape); The Class "phylo4" (phylobase); The Class "matching" (ape); The Class "treeshape" (apTreeshape); The Class "haploNet" (pegas); 3.1.2 Networks; 3.1.3 Splits; 3.1.4 Molecular Sequences; The Class "DNAbin" (ape); The Class "haplotype" (pegas); The Class "alignment" (seqinr); The Class "phyDat" (phangorn); 3.1.5 Allelic Data; The Class "loci" (pegas); The Class "genind" (adegenet); The Classes "SNPbin" and "genlight" (adegenet)3.1.6 Phenotypic Data; 3.2 Reading Phylogenetic Data; 3.2.1 Phylogenies; 3.2.2 Molecular Sequences; 3.2.3 Allelic Data; 3.2.4 Reading Data Over the Internet; 3.3 Writing Data; 3.4 Manipulating Data; 3.4.1 Basic Tree Manipulation; 3.4.2 Rooted Versus Unrooted Trees; 3.4.3 Graphical Tree Manipulation; 3.4.4 Dichotomous Versus Multichotomous Trees; 3.4.5 Summarizing and Comparing Trees; 3.4.6 Manipulating Lists of Trees; 3.4.7 Molecular Sequences; 3.4.8 Allelic Data; 3.5 Converting Objects; 3.6 Managing Labels and Linking Data Sets; 3.7 Sequence Alignment3.8 Case Studies; 3.8.1 Sylvia Warblers; 3.8.2 Mammalian Mitochondrial Genomes; 3.8.3 ButterflyDNA Barcodes; 3.9 Exercises; 4 Plotting Phylogenies; 4.1 Simple Tree Drawing; 4.1.1 Node, Tip and Edge Annotations; 4.1.2 Axes and Scales; 4.1.3 Manual and Interactive Annotation; 4.1.4 Showing Clades; 4.1.5 Plotting Phylogenetic Variables; 4.2 Combining Plots; 4.2.1 Tree{Variable Coplot; 4.2.2 Cophylogenetic Plot; 4.3 Large Phylogenies; 4.4 Networks; 4.5 Data Exploration with Animations; 4.6 Exercises; 5 Phylogeny Estimation; 5.1 Distance Methods; 5.1.1 Calculating Distances; Classical DistancesEvolutionary Distances; Special Distances; 5.1.2 Exploring and Assessing Distances; 5.1.3 Simple Clustering, UPGMA, and WPGMA; 5.1.4 Neighbor-Joining; 5.1.5 Extensions of Neighbor-Joining: UNJ and BIONJ; 5.1.6 Minimum Evolution; 5.2 Maximum Likelihood Methods; 5.2.1 Substitution Models: A Primer; Jukes and Cantor 1969 (JC69); Kimura 1980 (K80); Felsenstein 1981 (F81); Kimura 1981 (K81); Felsenstein 1984 (F84); Hasegawa, Kishino, and Yano 1985 (HKY85); Tamura 1992 (T92); Tamura and Nei 1993 (TN93); The General Time-Reversible Model (GTR); Barry and Hartigan 1987, LogDet, and Paralinear....
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