Package: MSA2dist
Type: Package
Title: MSA2dist calculates pairwise distances between all sequences of
        a DNAStringSet or a AAStringSet using a custom score matrix and
        conducts codon based analysis
Version: 1.15.0
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.
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, 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
SystemRequirements: C++11
URL: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist,
        https://mpievolbio-it.pages.gwdg.de/MSA2dist/
BugReports: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist/issues
RoxygenNote: 7.3.1
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:14:34 UTC
RemoteUrl: https://github.com/bioc/MSA2dist
RemoteRef: HEAD
RemoteSha: 662eead598a4698ac0fb563ed39e1fe2bd0f2204
Packaged: 2026-01-30 08:18:31 UTC; root
Author: Kristian K Ullrich [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4308-9626>)
Maintainer: Kristian K Ullrich <ullrich@evolbio.mpg.de>
Built: R 4.6.0; x86_64-apple-darwin20; 2026-01-30 08:22:33 UTC; unix
