I have been working with Dr. Holder on a phylogenetic question, to develop an efficient algorithm for calculating pattern class probabilities on evolutionary trees. We developed this algorithm, and submitted it to PLOS Currents Tree of Life for publication. We are currently developing a specialization of the algorithm for symmetric cases, in which all states are equivalent. This work is being conducted in open source software written in C++, and all results and notes are visible at https://github.com/mtholder/PhyPatClassProb.
Next semester I hope to apply our algorithms to a variety of datasets, and to calculate goodness-of-fit statistics from our algorithms' computed probabilities in order to have a more rigorous test of model adequacy.
Department of Ecology & Evolutionary Biology
Haworth Hall, 900 Sunnyside Avenue
Lawrence, KS 66045