Schedule and Readings
Before Wednesday, 9 February:
- Read Chapter 19 – 26 of Hubert’s The DNA Book. (Chapter 26 on Mutations and Changes is the one most relevant to today’s class.)
- Read Chapter 5 of the Bioinformatics Algorithms: How do we compare biological sequences?.
Before Monday, 14 Feb:
- Chapter 26 of Manolis Kellis et al., Computational Biology - Genomes, Networks, and Evolution: Molecular Evolution and Phylogenetics (also available as [PDF]) (if you prefer to watch a video lecture that this chapter is based on, you can watch MIT CompBio Lecture 19 - Phylogenetics).
Thursday, 24 Feb:
Slides
The slides from the 9 February class are here: class7.pdf
Some links to materials for the class:
-
Georgia Ray (“Eukaryote Write Blog”), There’s no such thing as a tree (phylogenetically). May 2021.
-
Thomas Bayes, conveyed by Mr. Price, As Essay towards solving a Problem in the Doctrine of Chances, 1763. Biography of Bayes: D.R. Bellhouse, The Reverend Thomas Bayes, FRS: A Biography to Celebrate the Tercentenary of His Birth, 2004.
-
Recent New York Times articles about Bayesian reasoning: _How to Think Like an Epidemiologist, 4 August 2020; When They Warn of Rare Disorders, These Prenatal Tests Are Usually Wrong, 1 January 2022.
-
Russell D. Gray, Simon Greenhil and Robert M. Moss. The Pleasures and Perils of Darwinizing Culture (with phylogenies). 2007.
-
Fabrícia F. Nascimento, Mario dos Reis, and Ziheng Yang. A biologist’s guide to Bayesian phylogenetic analysis. Nature Ecology and Evolution, October 2017.