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 (3.20)
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("fastreeR")
):
Installation
To install this package, start R (version "4.4") 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")
fastreeR | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Clustering, Metagenomics, Phylogenetics, Software |
Version | 1.9.0 |
In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
License | GPL-3 |
Depends | R (>= 4.4) |
Imports | ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils |
System Requirements | Java (>= 8) |
URL | https://github.com/gkanogiannis/fastreeR https://github.com/gkanogiannis/BioInfoJava-Utils |
Bug Reports | https://github.com/gkanogiannis/fastreeR/issues |
See More
Suggests | BiocFileCache, BiocStyle, 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_1.9.0.tar.gz |
Windows Binary | fastreeR_1.9.0.zip |
macOS Binary (x86_64) | fastreeR_1.9.0.tgz |
macOS Binary (arm64) | fastreeR_1.9.0.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 |