Models and Algorithms for Genome Evolution

Part I: Emergence of Standard Algorithms What's Behind Blast Gene Myers Forty Years of Model-Based Phylogeography David Bryant and Jamie Kydd How to Infer Ancestral Genome Features by Parsimony Miklos Csuros Duplication, Rearrangement and Reconciliation Cedric Chauve, Nadia El-Mabrouk, Laurent Gueguen, Magali Semeria and Eric Tannier The Genesis of the DCJ Formula Anne Bergeron and Jens Stoye Part II: New Lights on Current Paradigms Large-Scale Multiple Sequence Alignment and Phylogeny Estimation Tandy Warnow Rearrangements in Phylogenetic Inference Bernard M.E. Moret, Yu Lin and Jijun Tang Status of Research on Insertion and Deletion Variations in the Human Population Liqing Zhang, Mingming Liu and Layne T. Watson A Retrospective on Genomic Preprocessing for Comparative Genomics Binhai Zhu A Comparison of DCJ and Algebraic Distances Joao Meidanis and Sophia Yancopoulos Part III: Promising Directions Fractionation, Rearrangement, Consolidation, Reconstruction David Sankoff and Chunfang Zheng Error Detection and Correction of Gene Trees Manuel Lafond, Krister M. Swenson and Nadia El-Mabrouk The Potential of Family-Free Genome Comparison Marilia D.V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thevenin and Roland Wittler Genetic History of PopulationsDaniel E. Platt, Filippo Utro, Marc Pybus and Laxmi Parida