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: 1.4.0
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 calcualtions which can be adapted to any scoring for DNA or AA
    characters. E.g. by using literal distances MSA2dist calculates pairwise
    IUPAC distances.
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: false
biocViews: Alignment, Sequencing, Genetics, GO
Depends: R (>= 4.2.0)
Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel,
        dplyr, foreach, methods, parallel, rlang, seqinr, stringr,
        tibble, tidyr, stats, stringi
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: 7.2.1
git_url: https://git.bioconductor.org/packages/MSA2dist
git_branch: RELEASE_3_17
git_last_commit: 1f16259
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
Packaged: 2023-04-25 21:50:30 UTC; biocbuild
Author: Kristian K Ullrich [aut, cre] (<https://orcid.org/0000-0003-4308-9626>)
Maintainer: Kristian K Ullrich <ullrich@evolbio.mpg.de>
Built: R 4.3.0; x86_64-conda-linux-gnu; 2023-07-11 18:03:57 UTC; unix
