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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 2.3.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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, 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_2.3.0.tar.gz |
| Windows Binary (x86_64) | fastreeR_2.3.0.zip |
| macOS Binary (big-sur-x86_64) | fastreeR_2.3.0.tgz |
| macOS Binary (sonoma-arm64) | fastreeR_2.3.0.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 |