fastreeR

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

Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.fastreeR

Bioconductor version: Release (3.22)

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 iD 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")

fastreeR HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, Metagenomics, Phylogenetics, Software

Version 2.0.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 years)

License GPL-3

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

Suggests BiocFileCache, BiocStyle, ggtree, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package fastreeR_2.0.0.tar.gz

Windows Binary (x86_64) fastreeR_1.99.4.zip (64-bit only)

macOS Binary (x86_64) fastreeR_2.0.0.tgz

macOS Binary (arm64) fastreeR_2.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/fastreeR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fastreeR

Bioc Package Browser https://code.bioconductor.org/browse/fastreeR/

Package Short Url https://bioconductor.org/packages/fastreeR/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.22 Source Archive