MIT CompBio Lecture 19 - Phylogenetics

MIT Computational Biology: Genomes, Networks, Evolution, Health Prof. Manolis Kellis http://compbio.mit.edu/6.047/ Fall 2018 Lecture 18 - Phylogenetics 0. Basics of phylogeny: Introduction and definitions Characters, traits, nodes, branches, lineages, topology, lengths Gene trees, species trees, cladograms, chronograms, phylograms 1. From alignments to distances: Modeling sequence evolution Turning pairwise sequence alignment data into pairwise distances Probabilistic models of divergence: Jukes Cantor/Kimura/hierarchy 2. From distances to trees: Tree-building algorithms Tree types: Ultrametric, Additive, General Distances Algorithms: UPGMA, Neighbor Joining, guarantees and limitations Optimality: Least-squared error, minimum evolution (require search) 3. From alignments to trees: Alignment scoring given a tree Parsimony: greedy (union/intersection) vs. DP (summing cost) ML/MAP (includes back-mutations, lengths): peeling algorithm (DP) 4. Tree exploration: Markov Chain Monte Carlo tree search Proposal operations: NNI neighbor interchange, SPR prune/regraft MCMC: Metropolis-Hastings, sample posterior P(B,T|D) without P(D) Lecture 19 slides: https://stellar.mit.edu/S/course/6/fa...