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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "MSA2dist" in publications use:'
type: software
license: GPL-3.0-only
title: 'MSA2dist: MSA2dist calculates pairwise distances between all sequences of
  a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based
  analysis'
version: 1.16.0
doi: 10.32614/CRAN.package.MSA2dist
identifiers:
- type: url
  value: https://mpievolbio-it.pages.gwdg.de/MSA2dist/
abstract: 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.
authors:
- family-names: Ullrich
  given-names: Kristian K
  email: ullrich@evolbio.mpg.de
  orcid: https://orcid.org/0000-0003-4308-9626
repository: https://bioc-release.r-universe.dev
commit: 4f21e42972dbdd2d8f2d1f6631ddd430032a5989
url: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist
date-released: '2026-04-28'
contact:
- family-names: Ullrich
  given-names: Kristian K
  email: ullrich@evolbio.mpg.de
  orcid: https://orcid.org/0000-0003-4308-9626