Programs

Current

I have a deep love of programming and am lucky to be able to integrate it into my research. In the course of my PhD I've written three programs to manipulate phylogenetic trees:
(Please note that the links will take you to the desktop version of my website!)

• TreeCollapser - Allows the user to re-root a tree, measure the root-to-tip length and average support value for each tip, and collapse bifurcations with support values below a supplied threshold to polytomies. It can also output trees with support values removed. I use this program in my current research on the heritability of virulence in HIV.
  
  
• ClusterMatcher - Allows monophyletic 'clusters' of closely-related sequences in a tree to be identified based on size or specified attributes. It also allows clusters that share sequences between two different trees (two different time points, or two different tree-building methods) to be matched, and selected based specified attributes.
  
  
• PareTree - A simple program that allows users to 'pare' down their trees by removing either unwanted sequences/tips, bootstrap values, or branch lenths - or any combination of the three - quickly and easily.