Objectives By the end of this week, you will: Have RAxML installed Be able to do an analysis with likelihood with various models Understand partitioning Be able to use a variety of character types Understand the basics of likelihood, parsimony, and Bayesian approaches Read papers This is a case where there are some good, readable, important overviews in the literature. Please read the ones listed at Pay the most attention to the Lewis 2001 TREE article. RAxML (Stamatakis, 2014) is a very popular program for inferring phylogenies using likelihood, though there are many others. It is notable for being able to […]

Week 3: Likelihood, Parsimony, and Bayesian approaches

Many of my students could do work on GitHub Classroom; some got an error and had to fork a repo instead. The only ones who ended up committing changes as pull requests back were those who did the forking; the Classroom students didn’t seem to do this. I’ll dig into why, but overall, seems like just using regular repos one forks works better for now. GitHub Classroom looks like it has potential, especially as this class scales up, so I’ll check it out again next year.

Leaving GitHub classroom