The aphylo R package implements estimation and data imputation methods for Functional Annotations in Phylogenetic Trees. The core function consists on the computation of the log-likelihood of observing a given phylogenetic tree with functional annotation on its leafs, and probabilities associated to gain and loss of functionalities, including probabilities of experimental misclassification. Furthermore, the log-likelihood is computed using peeling algorithms, which required developing and implementing efficient algorithms for re-coding and preparing phylogenetic tree data so that can be used with the package. Finally, aphylo works smoothly with popular tools for analysis of phylogenetic data such as ape R package, “Analyses of Phylogenetics and Evolution”.
More details here.