MSA2dist

DOI: 10.18129/B9.bioc.MSA2dist  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MSA2dist.

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Bioconductor version: 3.17

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.

Author: Kristian K Ullrich [aut, cre]

Maintainer: Kristian K Ullrich <ullrich at evolbio.mpg.de>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSA2dist")

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("MSA2dist")

 

HTML	R Script	MSA2dist Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, GO, Genetics, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2.0)
Imports	Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, rlang, seqinr, stringr, tibble, tidyr, stats, stringi
LinkingTo	Rcpp, RcppThread
Suggests	rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
SystemRequirements	C++11
Enhances
URL	https://gitlab.gwdg.de/mpievolbio-it/MSA2dist https://mpievolbio-it.pages.gwdg.de/MSA2dist/
BugReports	https://gitlab.gwdg.de/mpievolbio-it/MSA2dist/issues
Depends On Me
Imports Me	doubletrouble
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MSA2dist_1.4.0.tar.gz
Windows Binary	MSA2dist_1.4.0.zip
macOS Binary (x86_64)	MSA2dist_1.4.0.tgz
macOS Binary (arm64)	MSA2dist_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSA2dist
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSA2dist
Bioc Package Browser	https://code.bioconductor.org/browse/MSA2dist/
Package Short Url	https://bioconductor.org/packages/MSA2dist/
Package Downloads Report	Download Stats