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QuartetNetworkGoodnessFit

julia package for phylogenetic networks analyses using 4-taxon subsets.

https://github.com/juliaphylo/quartetnetworkgoodnessfit.jl

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (7.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

julia package for phylogenetic networks analyses using 4-taxon subsets.

Basic Info
  • Host: GitHub
  • Owner: JuliaPhylo
  • License: other
  • Language: Julia
  • Default Branch: master
  • Homepage:
  • Size: 604 KB
Statistics
  • Stars: 9
  • Watchers: 2
  • Forks: 1
  • Open Issues: 2
  • Releases: 12
Created over 6 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

doc: stable doc: dev Build status Coverage Code Style: Blue ColPrac: Contributor's Guide on Collaborative Practices for Community Packages PkgEval

overview

QuartetNetworkGoodnessFit, aka "Quarnet GoF" or simply "QGoF", is a Julia package for phylogenetic networks analyses using four-taxon subsets. It includes tools to measure the goodness of fit of a phylogenetic network to data on subsets of 4 tips. It depends on the PhyloNetworks package.

citing

See CITATION.bib for the relevant reference(s).

Owner

  • Name: JuliaPhylo
  • Login: JuliaPhylo
  • Kind: organization

Citation (CITATION.bib) 

% reference for the package
@misc{QuartetNetworkGoodnessFit.jl,
  author  = {Cécile Ané <cecileane@users.noreply.github.com> and contributors},
  title   = {QuartetNetworkGoodnessFit.jl: Julia package for phylogenetic networks analyses using four-taxon subsets},
  url     = {https://github.com/JuliaPhylo/QuartetNetworkGoodnessFit.jl},
  version = {v0.5.1},
  year    = {2023},
}
% reference for the goodness-of-fit test
@article{2021CaiAne,
    author  = {Ruoyi Cai & C{\'e}cile An{\'e}},
    title = {Assessing the fit of the multi-species network coalescent to multi-locus data},
    year = {2021},
    journal = {Bioinformatics},
    volume = {37},
    number = {5},
    pages = {634-641},
    doi = {10.1093/bioinformatics/btaa863},
}
% reference for the algorithm to calculate expected quartet concordance factors
@article{2024AFABR-anomalous,
    author = {C{\'e}cile An{\'e} and John Fogg and Elizabeth S. Allman and
      Hector Ba{\~n}os and John A. Rhodes},
    title = {Anomalous networks under the multispecies coalescent: theory and prevalence},
    year = {2024},
    journal = {Journal of Mathematical Biology},
    volume = {88},
    pages = {29},
    doi = {10.1007/s00285-024-02050-7},
}
% reference for the simulation package and the correlated inheritance model
@article{2023fogg_phylocoalsimulations,
  author = {Fogg, John and Allman, Elizabeth S and An{\'e}, C{\'e}cile},
  title = {{PhyloCoalSimulations}: A simulator for network multispecies coalescent
        models, including a new extension for the inheritance of gene flow},
  journal = {Systematic Biology},
  year = {2023},
  volume = {72},
  number = {5},
  pages = {1171-1179},
  doi = {10.1093/sysbio/syad030},
}

GitHub Events

Total
  • Delete event: 3
  • Issue comment event: 2
  • Push event: 6
  • Pull request event: 3
  • Create event: 2
  • Commit comment event: 2
Last Year
  • Delete event: 3
  • Issue comment event: 2
  • Push event: 6
  • Pull request event: 3
  • Create event: 2
  • Commit comment event: 2

Packages

  • Total packages: 1
  • Total downloads:
    • julia 2 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 12
juliahub.com: QuartetNetworkGoodnessFit

julia package for phylogenetic networks analyses using 4-taxon subsets.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2 Total
Rankings
Dependent repos count: 9.9%
Average: 34.5%
Stargazers count: 35.6%
Dependent packages count: 38.9%
Forks count: 53.5%
Last synced: 6 months ago

Dependencies

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