Inferring Gene Trees

This repository contains tutorials for learning about maximum likelihood (ML) and Bayesian inference of trees from individual genes. For ML inference, we will use IQTree. For Bayesian inference, we will use RevBayes. AliView will also be helpful to view sequence alignments, and FigTree will be helpful to view trees. Finally, a software tool called (Tracer)[https://github.com/beast-dev/tracer/releases/tag/v1.7.2] is useful for diagnosing the performance of our MCMC based analyses.

• Maximum likelihood inference (general)
  • Genetic Distance
• Maximum likelihood inference (phylogenies)
  • Fixed Model of Sequence Evolution
• Nonparametric bootstrapping
  • Phylogenetic Bootstrapping
• Bayesian inference with Markov chain Monte Carlo (general)
  • Mean of a Normal
  • Introduction to Graphical Models
  • Estimating p for a binomial (using a graphical model)
• Bayesian inference with MCMC (phylogenies)
  • Phylogenetic MCMC with a Fixed Model
  • Debugging your Markov chain Monte Carlo (MCMC) and a related paper. Using RWTY to assess convergence and mixing for topologies.