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phangorn R Package

repository·main·Indexed 42 days ago

https://github.com/klausvigo/phangorn

A comprehensive R package for phylogenetic reconstruction and analysis. It supports distance-based methods, Maximum Parsimony, and Maximum Likelihood models, including advanced mixture and partition models, Hadamard conjugation, character data simulation, and congruence analyses.

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What's inside phangorn

  1. Overview of phangorn capabilities

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    phangorn is an R package designed for phylogenetic reconstruction and analysis. It supports several key methodologies and tasks:

    • Reconstruction Methods: Distance-based methods, Maximum Parsimony, and Maximum Likelihood (ML).
    • Advanced ML Modeling: Estimation of mixture and partition models by extending the general ML framework.
    • Mathematical Operations: Performing Hadamard conjugation.
    • Analysis & Comparison: Exploring and comparing trees, phylogenetic models, or splits.
    • Simulation & Congruence: Simulating character data and performing congruence analyses.

  2. Learn phylogenetic inference with the 'Trees' vignette

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    For a practical introduction to phylogenetic inference using phangorn, run the following command in your R session to view the official vignette:

    vignette("Trees", package="phangorn")

  3. Install phangorn

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    You can install phangorn from CRAN for the stable release, or via GitHub/r-universe for the development version.

    If you are installing the development version, you may need to install the Biostrings package from Bioconductor first. To access all available functionality, it is recommended to also install rgl and ggseqlogo.

    # Install Release version from CRAN
install.packages("phangorn")

# Install Development version from GitHub
remotes::install_github("KlausVigo/phangorn")

# Install Development version from r-universe
install.packages('phangorn', repos = c('https://klausvigo.r-universe.dev', 'https://repo.r-wasm.org'))

# Prerequisite for development version
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Biostrings")

# Recommended for full functionality
install.packages("rgl")
install.packages("ggseqlogo")