MSA2dist
This is the released version of MSA2dist; for the devel 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: Release (3.23)
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 calculations which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions (dN/dS) in a parallelised fashion using a variety of substitution models. Non-aligned coding sequences can be directly used to construct pairwise codon alignments (global/local) and calculate dN/dS without any external dependencies.
Author: Kristian K Ullrich [aut, cre] 
Maintainer: Kristian K Ullrich <ullrich at evolbio.mpg.de>
citation("MSA2dist")):Kristian K Ullrich. MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. doi:10.18129/B9.bioc.MSA2dist, R package version 1.16.0, https://bioconductor.org/packages/MSA2dist.
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")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, GO, Genetics, Sequencing, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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, rhinotypeR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSA2dist_1.16.0.tar.gz |
| Windows Binary (x86_64) | MSA2dist_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | MSA2dist_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | MSA2dist_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSA2dist |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSA2dist |
| Package Short Url | https://bioconductor.org/packages/MSA2dist/ |
| Package Downloads Report | Download Stats |