Evolutionary Genomics

Statistical and Computational Methods, Volume 1

Editors:

ISBN: 978-1-61779-581-7 (Print) 978-1-61779-582-4 (Online)

Table of contents (16 protocols)

  1. Front Matter

    Pages i-xiv

  2. Introduction: Bioinformatician’s Primers

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 3-49

      Introduction to Genome Biology: Features, Processes, and Structures

    3. Book Protocol

      Pages 51-76

      Diversity of Genome Organisation

    4. No Access

      Book Protocol

      Pages 77-110

      Probability, Statistics, and Computational Science

    5. No Access

      Book Protocol

      Pages 111-152

      The Essentials of Computational Molecular Evolution

  3. Genomic Data Assembly, Alignment, and Homology Inference

    1. Front Matter

      Pages 153-153

    2. No Access

      Book Protocol

      Pages 155-174

      Next-Generation Sequencing Technologies and Fragment Assembly Algorithms

    3. No Access

      Book Protocol

      Pages 175-201

      Gene Prediction

    4. No Access

      Book Protocol

      Pages 203-235

      Alignment Methods: Strategies, Challenges, Benchmarking, and Comparative Overview

    5. No Access

      Book Protocol

      Pages 237-257

      Whole-Genome Alignment

    6. No Access

      Book Protocol

      Pages 259-279

      Inferring Orthology and Paralogy

    7. No Access

      Book Protocol

      Pages 281-308

      Detecting Laterally Transferred Genes

  4. Genome Evolution: Insights from Statistical Analyses

    1. Front Matter

      Pages 309-309

    2. No Access

      Book Protocol

      Pages 311-335

      Genome Evolution in Outcrossing Versus Selfing Versus Asexual Species

    3. No Access

      Book Protocol

      Pages 337-359

      Transposable Elements and Their Identification

    4. No Access

      Book Protocol

      Pages 361-383

      Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

    5. No Access

      Book Protocol

      Pages 385-395

      Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications

    6. No Access

      Book Protocol

      Pages 397-429

      Analysis of Gene Order Evolution Beyond Single-Copy Genes

    7. No Access

      Book Protocol

      Pages 431-455

      Discovering Patterns in Gene Order

  5. Back Matter

    Pages 457-467