UC Berkeley Grad Seminar in Phylogenetics
Markdown is useful for editing this website and others as well as writing reports.
Git is version control software. It is awesome for collaborating and keeping track of different versions of a project’s files. Use it for your code and even your papers. GitHub is a web-based interface for Git.
To perform statistical phylogenetic analyses it helps to understand the basic principles of statistical analysis and probability, especially Bayesian statistics. Here is a brief tutorial that conveys the basic ideas:
Many bioinformatic and phylogenetic tools are run from the command line. Try using the command prompt and familiarize yourself with the following commands:
Try this simple Unix tutorial if you need more guidance: http://matt.might.net/articles/basic-unix/
R is super useful for performing analyses and visualizing results:
A very short introduction to R
You should familiarize yourself a little with the basic ideas behind Bayesian phylogenetics. Here are three great papers that should introduce you to the topic if you are not familiar yet.
We’re a bit biased about what phylogenetic software you should use. Many different types of phylogenetic analyses can be performed directly in RevBayes and the tutorials explain the models and how to set them up.
Here are some other programs that can be useful: