Introduction to Genome Biology: Features, Processes, and Structures.- Diversity of Genome Organization.- Probability, Statistics, and Computational Science.- The Essentials of Computational Molecular Evolution.- Next-Generation Sequencing Technologies and Fragment Assembly Algorithms.- Gene Prediction.- Alignment Methods: Strategies, Challenges, Benchmarking, and Comparative Overview.- Whole-Genome Alignment.- Inferring Orthology and Paralogy.- Detecting Laterally Transferred Genes.- Genome Evolution in Outcrossing Vs. Selfing Vs. Asexual Species.- Transposable Elements And Their Identification.- Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans.- Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications.- Analysis of Gene Order Evolution Beyond Single-Copy Genes.- Discovering Patterns in Gene Order.