fastreeR

DOI: 10.18129/B9.bioc.fastreeR  

Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	fastreeR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, Metagenomics, Phylogenetics, Software
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
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_1.2.0.tar.gz
Windows Binary	fastreeR_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	fastreeR_1.2.0.tgz
macOS Binary (arm64)	fastreeR_1.2.0.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