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Cited by 71Genomics and Phylogenetic StudiesBacterial Genetics and BiotechnologyBioinformatics and Genomic Networks

Coinfinder: detecting significant associations and dissociations in pangenomes

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Whelan, Fiona Jane, Rusilowicz, Martin, McInerney, James Oscar·2020·Microbial Genomics
DOI 10.1099/mgen.0.000338PMC PMC7200068

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Abstract

The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are ‘coincident’) more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.

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  • Controlling for confounding variables such as phylogeny does not reduce statistical power.

    “Controlling for confounding variables such as phylogeny does not reduce statistical power, because such variables should be accounted for before making any estimates of power18,114,115.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [114]

    The Theory and implementation section describes how Coinfinder assesses phylogenetic lineage-dependence, but does not compare statistical power with and without that assessment. The Results section discusses how Coinfinder’s power varies with dataset size and gene diversity, not whether controlling for phylogeny reduces power or should precede power estimates. No page numbers are available in our copy. (LLM, conf=0.75)

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Cited by

Sorted by citations

Authors
Whelan, F. J., Rusilowicz, M., & McInerney, J. O.
Affiliations
  • University of Nottingham (GB)
  • University of Manchester (GB)
Corresponding author
McInerney, James Oscar
ORCID
Venue
Microbial Genomics
Publisher
Microbiology Society
Published
2020-03-01
Volume
6
Issue
3
ISSN
2057-5858 (ISSN-L)
DOI
10.1099/mgen.0.000338
PMC
PMC7200068
OpenAlex
W3008753509
Cited by
71
References
1
Citations by year
2026: 11 · 2025: 12 · 2024: 12 · 2023: 11 · 2022: 13 · 2021: 10 · 2020: 1 · 2019: 1
FWCI
2.80
Type
journal article
Language
en
Open access
Licence
Locations
  • Microbial Genomics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Repository@Nottingham (University of Nottingham) (publishedVersion, cc-by)
  • Research Explorer (The University of Manchester) (publishedVersion, other-oa)
  • Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by-nc-nd)
  • Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by)
Funders
  • Biotechnology and Biological Sciences Research Council (BB/N018044/2)
  • H2020 Marie Skłodowska-Curie Actions (793818)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
pan-genome, accessory genes, gene co-occurrence, gene loss, horizontal gene transfer, phylogenetic distribution, prokaryotes, eukaryotes, statistical significance testing
MeSH terms
Phylogeny, Software, Streptococcus pneumoniae, Genome, Computational Biology

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