Section 2 : Phylogenetic analysis


Recordings

none


Textbook readings

Chapter 3, page 25


Notes, Comments and Updates

Comments

We'll go through how a phylogenetic analysis is performed, then go over trees, how they work, and what they mean, and some of the problems with them. There are 4 purposes for doing this:

  1. to demonstrate that phylogenetic trees are not magic (they are straightforward transformations of sequences into a graph showing how they are related by similarity), so that you can interpret them appropriately,

  2. to introduce you to some of the complications and alternative processes, so that you can recognize the importance of different approaches and parameters, and...

  3. to make you aware of some of the most important pitfalls in the process, so that you can think critically about phylogentic trees.

Updates

In previous years in this course, and in the textbook, the process of actually doing alignments and phylogenetic analysis are gone over in great detail - enough so that students were expected to be able to do simple examples themselves on paper, including on the first midterm exam. Because these are now covered insufficient detail in GN 311, we will cover these more superficially than in the past, and so these problems will not appear in problem sets or exams. Instead, we will focus more how to interpret and extract information from phylogenetic trees, In addition, we'll cover the tree-construction process used in the Ribosomal Database Project (Weighbor) as a great example, and one relevant to those of you taking MB 452 (Microbial Diversity Laboratory).