Package: MSA2dist
Type: Package
Title: MSA2dist calculates pairwise distances for
        DNAStringSet/AAStringSet using custom scoring, conducts codon
        analyses (including dNdS), and estimates Dxy/FST
Version: 1.17.8
Authors@R: 
    person(given = "Kristian K",
           family = "Ullrich",
           role = c("aut", "cre"),
           email = "ullrich@evolbio.mpg.de",
           comment = c(ORCID = "0000-0003-4308-9626"))
Description: 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. In addition, MSA2dist provides population genetic
        analyses, including the calculation of nucleotide divergence
        between populations (Dxy) and genetic differentiation
        statistics (FST) from aligned sequence data.
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: false
biocViews: Alignment, Sequencing, Genetics, GO
Depends: R (>= 4.4.0)
Imports: Rcpp, Biostrings, GenomicRanges, IRanges, MultipleAlignment,
        ape, doParallel, dplyr, foreach, methods, parallel, pwalign,
        rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils
Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
LinkingTo: Rcpp, RcppThread
VignetteBuilder: knitr
NeedsCompilation: yes
URL: https://github.com/kullrich/MSA2dist
BugReports: https://github.com/kullrich/MSA2dist/issues
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-26 21:52:06 UTC
RemoteUrl: https://github.com/bioc/MSA2dist
RemoteRef: HEAD
RemoteSha: bf677287ca98daddecd2381a95149e25cf5f9d93
Packaged: 2026-06-27 06:37:14 UTC; root
Author: Kristian K Ullrich [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4308-9626>)
Maintainer: Kristian K Ullrich <ullrich@evolbio.mpg.de>