2017 - 2019

The goal of the Acceptability model project was to propose a new model of protein evolution based on the assumption that the propensity for each amino acid at a site changes over time. Most previous models either required the amino acid propensities to be unchanging with time or to only change at specific points on the tree. Although it is much more difficult to design and test a model that changes continuously, that was precisely the goal of this project.

Due to the complexity of the model, previous common techniques for model testing could not be used and different methods were necessary. I implemented this new model and the effecient way to optimize the model in a Perl program. I successfully showed that this model can detect subtle shifts in amino acid propensities and can even highlight how the substitutions in a protein can shift the propensities of nearby sites.

Repository: https://publichg.stephentpollard.com/CovarionSimulation