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aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees
Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).
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Package details |
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| Author | George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), USC Biostatistics [cph] |
| Maintainer | George Vega Yon <g.vegayon@gmail.com> |
| License | MIT + file LICENSE |
| Version | 0.3-4 |
| URL | https://github.com/USCbiostats/aphylo |
| Package repository | View on CRAN |
| Installation |
Install the latest version of this package by entering the following in R:
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