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. `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  0.0.99 
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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