MSA2dist

This is the development version of MSA2dist; for the stable 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: Development (3.20)

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>

Citation (from within R, enter citation("MSA2dist")):

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("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")
MSA2dist Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, GO, Genetics, Sequencing, Software
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3 + file LICENSE
Depends R (>= 4.4.0)
Imports Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils
System Requirements C++11
URL https://gitlab.gwdg.de/mpievolbio-it/MSA2dist https://mpievolbio-it.pages.gwdg.de/MSA2dist/
Bug Reports https://gitlab.gwdg.de/mpievolbio-it/MSA2dist/issues
See More
Suggests rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
Linking To Rcpp, RcppThread
Enhances
Depends On Me
Imports Me doubletrouble
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MSA2dist_1.9.0.tar.gz
Windows Binary MSA2dist_1.9.0.zip
macOS Binary (x86_64) MSA2dist_1.9.0.tgz
macOS Binary (arm64) MSA2dist_1.9.0.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/
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