MSA2dist
This is thereleased version of MSA2dist; for the devel version, seeMSA2dist.
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 (3.22)
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]
ORCID: 0000-0003-4308-9626
Maintainer: Kristian K Ullrich <ullrich at evolbio.mpg.de>
citation("MSA2dist")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("MSA2dist")For older versions of R, please refer to the appropriateBioconductor 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 | 1.14.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 years) |
| License | GPL-3 + fileLICENSE |
| 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/MSA2disthttps://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 |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | MSA2dist_1.14.0.tar.gz |
| Windows Binary (x86_64) | MSA2dist_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | MSA2dist_1.14.0.tgz |
| macOS Binary (arm64) | MSA2dist_1.14.0.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 |