Evolutionary genomics : statistical and computational methods. Volume 2 / edited by Maria Anisimova. — New York : Humana Press : Springer, c2012. – (58.17/m592/V.856)

Contents

    CONTENTS
    
    Preface
    Contributors
    PART I PHYLOGENOMICS
    1 Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Noncoalescent Genes
    2 Modeling Gene Family Evolution and Reconciling Phylogenetic Discord
    3 Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life
    4 Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns
    PART II NATURAL SELECTION， RECOMBINATION， AND INNOVATION IN GENOMIC SEQUENCES
    5 Selection on the Protein-Coding Genome
    6 Methods to Detect Selection on Noncoding DNA
    7 The Origin and Evolution of New Genes 161
    8 Evolution of Protein Domain Architectures 187
    9 Estimating Recombination Rates from Genetic Variation in Humans
    10 Evolution of Viral Genomes: Interplay Between Selection， Recombination， and Other Forces 239
    PART III POPULATION GENOMICS
    11 Association Mapping and Disease: Evolutionary Perspectives..
    12 Ancestral Population Genomics
    13 Nonredundant Representation of Ancestral Recombinations Graphs
    PART IV THE "-OMICS"
    14 Using Genomic Tools to Study Regulatory Evolution
    15 Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks
    16 Statistical Methods in Metabolomics
    17 Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
    18 Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases
    19 Genetical Genomics for Evolutionary Studies
    PART V HANDLING GENOMIC DATA: RESOURCES AND COMPUTATION
    20 Genomics Data Resources: Frameworks and Standards
    21 Sharing Programming Resources Between Bio* Projects Through Remote Procedure Call and Native Call Stack Strategies 513
    22 Scalable Computing for Evolutionary Genomics
    Index