DESCRIPTION

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: 1.11.1
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 (>= 4.4.0)
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