aphylo

CRANaphyloMaRDI QIDQ83700FDOQ83700

Statistical Inference and Prediction of Annotations in Phylogenetic Trees

George G. Vega Yon

Last update: 7 September 2023

Copyright license: MIT license, File License

Software version identifier: 0.3-2, 0.2-1, 0.3-1, 0.3-3

Description

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).

Cites work

• Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees

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