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Primer

Paul Lewis
University of Connecticut

Primer part 2: tree likelihood and rate heterogeneity

Paul Lewis
Paul Lewis

This series of 4 talks will be an introduction to phylogenetics in 4 parts from master expositor Paul Lewis.

Part 2 explains how the likelihood is calculated for trees, how parameters of models are estimated, and how missing data and unknown ancestral states are accommodated. This part ends with an introduction to three major ways of modeling among site rate heterogeneity (site-specific rates and the +I and +G models).

Paul Lewis
University of Connecticut

Primer part 3a: introduction to Bayesian statistics

This series of 4 talks will be an introduction to phylogenetics in 4 parts from master expositor Paul Lewis.

Part 3 is an introduction to Bayesian statistics and how it is used in phylogenetics. This part is divided into parts 3a and 3b. Part 3a explains Bayes Rule, the difference between probabilities and probability densities, the difference between joint, conditional and marginal probabilities, and illustrates how MCMC is used to approximate posterior probability distributions.

Paul Lewis
University of Connecticut

Primer part 3b: introduction to Bayesian phylogenetics

This series of 4 talks will be an introduction to phylogenetics in 4 parts from master expositor Paul Lewis.

Part 3b continues part 3a with proposals (updating model parameters or trees during MCMC), prior distributions, hierarchical models, and Bayes factors.