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]
Maintainer: Anestis Gkanogiannis <anestis at gkanogiannis.com>
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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, Metagenomics, Phylogenetics, Software |
| Version | 1.12.5 |
| 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 |
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_1.12.5.tar.gz |
| Windows Binary (x86_64) | fastreeR_1.12.5.zip (64-bit only) |
| macOS Binary (x86_64) | fastreeR_1.12.5.tgz |
| macOS Binary (arm64) | fastreeR_1.12.5.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 3.21 | Source Archive |