Phylogenetic analysis - Creating phylogenetic trees


Recordings


Textbook readings

Chapter 4, pages 42-51


Notes, Comments and Updates

What's the point?

  1. To be able to describe how a phylgenetic tree from a sequence alignment using the Neighbor-joining method
  2. To be able to describe how a similarity matrix from an alignment
  3. To be able to describe how a distance matrix from a similarity matrix
  4. To be able to describe how the structure of a tree using the neighbor-joining method from a distance matrix
  5. To be able to describe how branch lengths within a tree are determined using the distance matrix
  6. To be able to describe what a "root" is and how it is included in a tree

Updates

In past years in this course, we've covered tree construction using the Neighbor-joining method in great detail. Because this process is now covered in detail in GN 311, it will be covered more quickly here, in concept rather than the level of detail required for students to perform this process manually, for example on exams. In other words, although I WILL expect you to be able to generate the structure of a tree using Neighborjoining, but will NOT expect you to be able to determine branch lengths (as described in the textbook) on an exam.