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Index
Cover
Front Matter
Part I. Introduction: Bioinformatician’s Primers
1. Introduction to Genome Biology and Diversity
2. Probability, Statistics, and Computational Science
3. A Not-So-Long Introduction to Computational Molecular Evolution
Part II. Genomic Alignment and Homology Inference
4. Whole-Genome Alignment
5. Inferring Orthology and Paralogy
6. Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics
Part III. Phylogenomics and Genome Evolution
7. Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model
8. Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life
9. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution
10. Bayesian Molecular Clock Dating Using Genome-Scale Datasets
11. Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species
Part IV. Natural Selection and Innovation in Genomic Sequences
12. Selection Acting on Genomes
13. Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship Between Model and Data
14. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
15. Evolution of Protein Domain Architectures
16. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans
Part V. Population Genomics and Omics in Light of Disease and Evolution
17. Association Mapping and Disease: Evolutionary Perspectives
18. Ancestral Population Genomics
19. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
20. Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials
21. Systems Genetics for Evolutionary Studies
Part VI. Handling Genomic Data: Resources and Computation
22. Semantic Integration and Enrichment of Heterogeneous Biological Databases
23. High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE
24. Scalable Workflows and Reproducible Data Analysis for Genomics
25. Sharing Programming Resources Between Bio* Projects
Back Matter
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