Department of Ecology and Evolutionary Biology
University of Kansas
1200 Sunnyside Ave
Lawrence KS 66045
I am currently working on methods for detecting and correcting a class of alignment errors: over compression. Each column in an alignment represents residues that should be inherited from a common ancestor. Under a strict interpretation of homology, each site in an alignment can be explained at most one insertion, but possibly multiple deletions. In a compressed alignment, residues inherited from an insertion event appear in the same column as residues that did not arise from that event. Our method compares site-likelihoods under a model that allows multiple insertions to site-likelihoods under a form of stochastic Dollo model which prohibits multiple insertions in the same column. Site-likelihood comparisons that favour multiple insertions can be used to guide the splitting of a single column into two or more columns in which all of the residues do appear to be homologous.
I started in Mark Holder's lab in November 2011 shortly after I completed my PhD at the University of Manchester
in the lab of Dr. Simon Whelan
. My PhD research was focused on two areas, linked by the common thread of phylogenetic trees:
- The Tree Search Problem - The number of possible phylogenetic trees grows super-exponentially with the number of taxa and this can make finding the tree that best fits the data very difficult. We investigated how often different methods find a “good” tree (one statistically indistinguishable from the best tree) and whether any features of the data are correlated with the difficulty of the tree search problem.
- Modelling Gene Family Evolution - Inferring gene family evolutionary is still in its infancy when compared to DNA or Protein evolution and models are still being developed. We investigated and compared the parsimony and maximum likelihood methods of inference and are currently finishing work on different models, including those with a sink state, that could be used for gene family evolution.
Previous to doing my PhD I completed a MSc in Bioinformatics, also at the University of Manchester. Between my first degree and my masters I worked for the UK Ministry of Defence near Bath, for five years. I obtained my first degree, a BSc in Computer Science, from the University of Wales, Swansea (now the University of Swansea).
- DupliphyML A tool for modelling gene family size evolution.
- GeLL A Java library for general likelihood calculations.