fastreeR

DOI: 10.18129/B9.bioc.fastreeR    

This is the development version of fastreeR; for the stable release version, see fastreeR.

Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Bioconductor version: Development (3.17)

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

Author: Anestis Gkanogiannis [aut, cre]

Maintainer: Anestis Gkanogiannis <anestis at gkanogiannis.com>

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

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script fastreeR
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, Metagenomics, Phylogenetics, Software
Version 1.3.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 years)
License GPL-3
Depends R (>= 4.2)
Imports ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils
LinkingTo
Suggests BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0)
SystemRequirements Java (>= 8)
Enhances
URL https://github.com/gkanogiannis/fastreeR https://github.com/gkanogiannis/BioInfoJava-Utils
BugReports https://github.com/gkanogiannis/fastreeR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package fastreeR_1.3.0.tar.gz
Windows Binary fastreeR_1.3.0.zip
macOS Binary (x86_64) fastreeR_1.3.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/fastreeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fastreeR
Package Short Url https://bioconductor.org/packages/fastreeR/
Package Downloads Report Download Stats

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