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 loglikelihood 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 misclasification. Furthermore, the loglikelihood is computed using Felsenstein's pruning algorithm, which required developing and implementing efficient algorithms for recoding 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".
Package details 


Maintainer  
License  MIT + file LICENSE 
Version  0.1.99 
URL  https://github.com/USCbiostats/phylogenetic 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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