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Bioconductor - fastreeR

fastreeR

This is the released version of fastreeR; for the devel version, see fastreeR.

Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Bioconductor version: Release (3.21)

Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java-11 and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.

Author: Anestis Gkanogiannis [aut, cre] ORCID: 0000-0002-6441-0688

Maintainer: Anestis Gkanogiannis <anestis at gkanogiannis.com>

Citation (from within R, enter citation("fastreeR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fastreeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("fastreeR")

Details biocViews Clustering, Metagenomics, Phylogenetics, Software Version 1.12.2 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License GPL-3.0-only Depends R (>= 4.4) Imports ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils System Requirements Java (>= 11) URL https://github.com/gkanogiannis/fastreeR https://github.com/gkanogiannis/BioInfoJava-Utils Bug Reports https://github.com/gkanogiannis/fastreeR/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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