Here you’ll find a compilation of tutorials I’ve put together, either for internal presentations with my lab or for conference presentations.
This tutorial is an introduction to constructing phylogenetic trees and covers common methods, the algorithmic processes behind them, and R code implementations so you can follow along! This should be a good tutorial for anyone new to phylogenetics that wants to dip their toes into the field.
This is a slightly more advanced tutorial put together for presentation at the Bioconductor 2022 conference in Seattle, WA. This tutorial introduces users to many common analyses by walking them through a complete computational pipeline for comparative genomics. Along the way, I demonstrate methods for sequence alignment, gene calling and annotation, finding clusters of orthologous genes, and building phylogenetic trees from sequencing data. Once we’ve covered all of those topics, we’ll use these methods (and some new software written by yours truly) to identify coevolving gene clusters from a dataset of sequencing data in order to predict novel gene function. This tutorial is more focused on code implementations than the Introduction to Phylogenetics tutorial.