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.
