From Gene Trees to a Species Tree - Starting from the Basics

Learn the fundamental concepts and advanced techniques for reconstructing species trees from gene trees in this comprehensive lecture from the Computational Genomics Summer Institute. Explore the theoretical foundations of phylogenetic reconstruction, beginning with basic principles and progressing to sophisticated algorithms for handling complex evolutionary scenarios. Discover how to address challenges in tree reconstruction including rooted tree consistency enhancement using max cut algorithms, quartet-based phylogenetic reconstruction methods, and compatibility analysis of quartet trees. Examine probabilistic approaches for recovering tree-like evolutionary patterns even in the presence of extensive lateral genetic transfer events. Gain insights into computational methods that bridge the gap between individual gene evolution and species-level phylogenetic relationships, with emphasis on both theoretical underpinnings and practical applications in genomic analysis.