Ebook: Models and Algorithms for Genome Evolution

Part I: Emergence of Standard Algorithms -- What's Behind Blast -- Forty Years of Model-Based Phylogeography -- How to Infer Ancestral Genome Features by Parsimony -- Duplication, Rearrangement and Reconciliation -- The Genesis of the DCJ Formula -- Part II: New Lights on Current Paradigms -- Large-Scale Multiple Sequence Alignment and Phylogeny Estimation -- Rearrangements in Phylogenetic Inference -- Status of Research on Insertion and Deletion Variations in the Human Population -- A Retrospective on Genomic Preprocessing for Comparative Genomics -- A Comparison of DCJ and Algebraic Distances -- Part III: Promising Directions -- Fractionation, Rearrangement, Consolidation, Reconstruction -- Error Detection and Correction of Gene Trees -- The Potential of Family-Free Genome Comparison -- Genetic History of Populations.