USCbiostats/phylogenetic: Statistical Inference of Annotated Phylogenetic Trees
Version 0.1.99

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".

Getting started

Package details

LicenseMIT + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
USCbiostats/phylogenetic documentation built on May 4, 2018, 2:27 p.m.