EPSRC Centre for Doctoral Training Cloud Computing for Big Data


Naomi Hannaford

PhD title

Complex Models in Phylogenetics

Research area

The aim of my project is to develop complex models for genetic sequence data eg alignments of DNA that incorporate more biological realism. I work with problems in phylogenetics and I am starting some research in the area of metagenomics.

Phylogenetics is the study of evolutionary history. It looks at relationships among different individuals or groups of organisms eg different species. The main goal of phylogenetic studies is to find a phylogenetic tree for a set of species (or organisms). A phylogenetic tree (similar to a family tree) is a graphical way of representing the evolutionary history of a set of species. It can tell us how all of the species of interest are related to each other.

The models I develop are statistical models for DNA evolution or more specifically substitutions in DNA sequences. These models are then used to analyse (real data sets of) DNA sequences from different species to learn what their phylogenetic tree is.

Existing standard models are not realistic, usually for computational convenience. Analysis with more complicated models takes longer to run. Thus, another aspect of my research is increasing computational speed of analysis. To do this, we aim to improve the software that we use via parallel computing and more efficient code.


Sarah Heaps, Tom Nye