MultipleAlignment
This is the development version of MultipleAlignment; to use it, please install the devel version of Bioconductor.
Representation of multiple sequence alignments in Bioconductor
Bioconductor version: Development (3.24)
The package implements a set of S4 classes (DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment) for representing Multiple Sequence Alignments (MSA). The classes allow users to represent groups of aligned DNA, RNA or amino acid sequences as a single object. The package also provides functions to read/write such object from/to traditional MSA file formats including Stockholm and Clustal.
Author: Marc Carlson [aut], Patrick Aboyoun [aut], Hervé Pagès [cre] 
, Beryl Kanali [ctb] (Converted 'MultipleAlignments' vignette from Sweave to RMarkdown), Michael Lawrence [ctb], Martin Morgan [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("MultipleAlignment")):Marc Carlson, Patrick Aboyoun. MultipleAlignment: Representation of multiple sequence alignments in Bioconductor. doi:10.18129/B9.bioc.MultipleAlignment, R package version 0.99.5, https://bioconductor.org/packages/MultipleAlignment.
Generated from the package metadata; it may differ from the package's own citation.
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("MultipleAlignment")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("MultipleAlignment")| Multiple Alignments | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, MultipleSequenceAlignment, Software |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | BiocGenerics (>= 0.59.10), S4Vectors, IRanges, Seqinfo, Biostrings |
| Imports | methods, stats |
| System Requirements | |
| URL | https://bioconductor.org/packages/MultipleAlignment |
| Bug Reports | https://github.com/Bioconductor/MultipleAlignment/issues |
See More
| Suggests | pwalign, testthat, knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | msa, rhinotypeR, rprimer |
| Imports Me | enhancerHomologSearch, GenomAutomorphism, MSA2dist, rfaRm |
| Suggests Me | BiocGenerics, Biostrings, ggmsa |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MultipleAlignment_0.99.5.tar.gz |
| Windows Binary (x86_64) | MultipleAlignment_0.99.5.zip |
| macOS Binary (big-sur-x86_64) | MultipleAlignment_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | MultipleAlignment_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MultipleAlignment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MultipleAlignment |
| Package Short Url | https://bioconductor.org/packages/MultipleAlignment/ |
| Package Downloads Report | Download Stats |