# --------------------------------------------
# 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 "syntenet" in publications use:'
type: software
license: GPL-3.0-only
title: 'syntenet: Inference And Analysis Of Synteny Networks'
version: 1.7.0
doi: 10.1093/bioinformatics/btac806
abstract: 'syntenet can be used to infer synteny networks from whole-genome protein
  sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm,
  which was ported to this package with the Rcpp framework for R and C++ integration.
  Anchor pairs from synteny analyses are treated as an undirected unweighted graph
  (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic
  profiling (by identifying which species contain which clusters) and; iii. microsynteny-based
  phylogeny reconstruction with maximum likelihood.'
authors:
- family-names: Almeida-Silva
  given-names: Fabrício
  email: fabricio_almeidasilva@hotmail.com
  orcid: https://orcid.org/0000-0002-5314-2964
- family-names: Zhao
  given-names: Tao
  email: tao.zhao@nwafu.edu.cn
  orcid: https://orcid.org/0000-0001-7302-6445
- family-names: Ullrich
  given-names: Kristian K
  email: ullrich@evolbio.mpg.de
  orcid: https://orcid.org/0000-0003-4308-9626
- family-names: Peer
  given-names: Yves
  name-particle: Van de
  email: yves.vandepeer@psb.vib-ugent.be
  orcid: https://orcid.org/0000-0003-4327-3730
preferred-citation:
  type: article
  title: 'syntenet: an R/Bioconductor package for the inference and analysis of synteny
    networks'
  authors:
  - family-names: Almeida-Silva
    given-names: Fabricio
  - family-names: Zhao
    given-names: Tao
    email: tao.zhao@nwafu.edu.cn
    orcid: https://orcid.org/0000-0001-7302-6445
  - family-names: Ullrich
    given-names: Kristian K.
  - family-names: Schranz
    given-names: M. Eric
  - family-names: Peer
    given-names: Yves
    name-particle: Van de
    email: yves.vandepeer@psb.vib-ugent.be
    orcid: https://orcid.org/0000-0003-4327-3730
  journal: Bioinformatics
  year: '2023'
  volume: '39'
  issue: '1'
  url: https://academic.oup.com/bioinformatics/article/39/1/btac806/6947985
  doi: 10.1093/bioinformatics/btac806
  start: btac806
repository: https://bioc.r-universe.dev
repository-code: https://github.com/almeidasilvaf/syntenet
url: https://support.bioconductor.org/t/syntenet
date-released: '2022-03-28'
contact:
- family-names: Almeida-Silva
  given-names: Fabrício
  email: fabricio_almeidasilva@hotmail.com
  orcid: https://orcid.org/0000-0002-5314-2964