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 analysisBioconductor version: Development (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 (from within R, entercitation("MSA2dist")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MSA2dist")Follow Installation instructions to use this package in your R session.
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