aphylo: Statistical Inference of Annotated Phylogenetic Trees

The aphylo R package implements a phylogenetic model for gene functional prediction that I have been developing as part of my doctoral disertation. The package includes functions for estimating these models including calculating probabilities of functional annotations on unannorated genes. This is part of a larger project on development of methods for Integrative Methods for Analysis of Genetic and Epidemiological Data (IMAGE) at USC.

More details here.