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 misclasification. Furthermore, the log-likelihood 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".
|License||MIT + file LICENSE|
|Package repository||View on GitHub|
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