Species and Gene Evolution

Huw A. Ogilvie

I am an Assistant Research Professor working in the Department of Computer Science here at Rice. My research is on the evolution of species and genes, as well as the development and progression of cancer, using phylogenetic methods.

COMP571 (Fall 2020, a.k.a. COVID times)

6 minute read

Important note: The information contained in the course syllabus, other than the absence policies, may be subject to change with reasonable advance notice, a...

Calculating the likelihood for an ultrametric tree (example)

5 minute read

In this example we will calculate the likelihood $P (D | T, h)$ where $D$ is a single site, $T$ is a rooted tree topology, and $h$ is the node heights fo...

Hill climbing and NNI

5 minute read

The Sankoff algorithm can efficiently calculate the parsimony score of a tree topology. Felsenstein’s pruning algorithm can efficiently calculate the probabi...

Long branch attraction (in the Felsenstein zone)

3 minute read

Long branch attraction is the phenomenon where two branches which are in truth not sisters are inferred to be sister branches when using maximum parsimony in...

Likelihood of a tree

7 minute read

The likelihood of a tree is the probability of a multiple sequence alignment or matrix of trait states (commonly known as a character matrix) given a tree to...