Manolis Kellis
@manoliskellis1·24.9K subscribers·255 videos
MIT CompBio Lecture 19 - Phylogenetics (Fall 2019)
Posted
November 12, 2019
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2,532
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November 12, 2019
2,532
45
1.78%
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1:20:37Now PlayingMIT Computational Biology: Genomes, Networks, Evolution, Health
Prof. Manolis Kellis
Full playlist with all videos in order is here
All slides from Fall 2019 are here
Outline for this lecture:
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)
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