Evolutionary Genomics

Statistical and Computational Methods, Volume 2

Editors:

ISBN: 978-1-61779-584-8 (Print) 978-1-61779-585-5 (Online)

Table of contents (22 protocols)

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  1. Front Matter

    Pages i-xv

  2. Phylogenomics

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 3-28

      Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Noncoalescent Genes

    3. No Access

      Book Protocol

      Pages 29-51

      Modeling Gene Family Evolution and Reconciling Phylogenetic Discord

    4. No Access

      Book Protocol

      Pages 53-79

      Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

    5. No Access

      Book Protocol

      Pages 81-110

      Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns

  3. Natural Selection, Recombination, and Innovation in Genomic Sequences

    1. Front Matter

      Pages 111-111

    2. No Access

      Book Protocol

      Pages 113-140

      Selection on the Protein-Coding Genome

    3. No Access

      Book Protocol

      Pages 141-159

      Methods to Detect Selection on Noncoding DNA

    4. No Access

      Book Protocol

      Pages 161-186

      The Origin and Evolution of New Genes

    5. No Access

      Book Protocol

      Pages 187-216

      Evolution of Protein Domain Architectures

    6. No Access

      Book Protocol

      Pages 217-237

      Estimating Recombination Rates from Genetic Variation in Humans

    7. No Access

      Book Protocol

      Pages 239-272

      Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

  4. Population Genomics

    1. Front Matter

      Pages 273-273

    2. No Access

      Book Protocol

      Pages 275-291

      Association Mapping and Disease: Evolutionary Perspectives

    3. No Access

      Book Protocol

      Pages 293-313

      Ancestral Population Genomics

    4. No Access

      Book Protocol

      Pages 315-332

      Nonredundant Representation of Ancestral Recombinations Graphs

  5. The "-omics"

    1. Front Matter

      Pages 333-333

    2. No Access

      Book Protocol

      Pages 335-361

      Using Genomic Tools to Study Regulatory Evolution

    3. No Access

      Book Protocol

      Pages 363-380

      Characterization and Evolutionary Analysis of Protein–Protein Interaction Networks

    4. No Access

      Book Protocol

      Pages 381-413

      Statistical Methods in Metabolomics

    5. No Access

      Book Protocol

      Pages 415-429

      Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN

    6. No Access

      Book Protocol

      Pages 431-467

      Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases

    7. No Access

      Book Protocol

      Pages 469-485

      Genetical Genomics for Evolutionary Studies

  6. Handling Genomic Data: Resources and Computation

    1. Front Matter

      Pages 487-487

    2. No Access

      Book Protocol

      Pages 489-511

      Genomics Data Resources: Frameworks and Standards

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