Why students would want to take this course and how it may help with future study/career opportunities: this course will be especially useful for student looking to continue in research involving evolution, phylogenies, and/or computational biology, as it will give you the knowledge and skills needed to begin research in these areas. More generally, you will gain skills in running open source software, command-line interfaces, dealing with sequence data, and visualising, analysing and processing biological data in R. These are job skills in the 21st century.
BIOSCI700: Phylogenetics will give students a thorough tour of modern phylogenetics: the models and methods behind sequence alignment and phylogenetic inference. The point of this course is go "under the hood" so that students learn the fundamentals of what is going on inside the "black box" of different computer programs. The course will also focus on "what we learn with phylogenies," i.e. using phylogenies to learn about the history of life, especially focusing on "macroevolution" -- evolution studied across clades rather than in individual populations. Modern macroevolution research is heavily based on model-based inference, so methods of inference (Maximum Likelihood, Bayesian), will be discussed along with the macroevolutionary models that are used. A key skill will be critical thinking about the assumptions of various models, because all models are relatively simple approximations of the fantastically complex and heterogeneous process of evolution, and we regularly discover that bad assumptions in our models can cause mistaken inference.
The practical work for the course will revolve around computer labs. The goal will be to have students develop the confidence to figure out how to get programs and analyses to run on their own computers, rather than be "hand held" with step-by-step instructions that will not be useful in future work with new or revised programs in the future. The macroevolutionary portion of the course will make use of R packages commonly used in the scientific literature.
This course replaces BIOINF 702: Comparative Bioinformatics, and covers similar topics (focusing on evolution & phylogenetics rather than e.g. protein structure or sequencing methods).