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PhyloTraits

Julia package for the analysis of trait evolution along a phylogeny, including phylogenetic networks.

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

Science Score: 57.0%

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    Found CITATION.cff file
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    Found 11 DOI reference(s) in README
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    Low similarity (12.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Julia package for the analysis of trait evolution along a phylogeny, including phylogenetic networks.

Basic Info
  • Host: GitHub
  • Owner: JuliaPhylo
  • License: mit
  • Language: Julia
  • Default Branch: main
  • Size: 659 KB
Statistics
  • Stars: 3
  • Watchers: 4
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created almost 2 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

PhyloTraits: trait evolution along phylogenies

|Documentation| Build Status | Code Coverage | Style Guide | |:---------------:|:----------------:|:-------------------:|:----------------| |stable dev | build PkgEval aqua | coverage | Code Style: Blue collaborative

Julia package for the analysis of trait evolution along a phylogeny, including phylogenetic networks. It depends on utilities from PhyloNetworks, from the JuliaPhylo project.

Quick start

To install & use the package, install Julia then type, within a Julia session: julia-repl julia> using PhyloTraits The first time, julia will prompt you for package installation.

Tutorials

  • Follow PhyloTraits's latest documentation. It includes a manual and examples of empirical analyses from the literature.
  • This tutorial is on comparative methods. It includes a tutorial for network calibration, which may be necessary prior to trait evolution analyses.

Citing

See CITATION.bib for the relevant reference(s). Below is a short list.

For continuous traits, analyses based on the Brownian motion process, with or without transgressive evolution after reticulations:

  • Bastide, Solís-Lemus, Kriebel, Sparks & Ané (2018). Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations. Systematic Biology, 67(5):800–820. doi:10.1093/sysbio/syy033. SI on dryad including a tutorial for trait evolution and a tutorial for network calibration.

Continuous traits, accounting for within-species variation:

  • Teo, Rose, Bastide & Ané (2023). Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. Bulletin of the Society of Systematic Biologists, 2(3):1-29. doi: 10.18061/bssb.v2i3.8977

For a discrete trait (influence of gene flow on the trait, ancestral state reconstruction, rates):

  • Karimi, Grover, Gallagher, Wendel, Ané & Baum (2020). Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Systematic Biology, 69(3):462-478. doi: 10.1093/sysbio/syz073.

[!NOTE] Much of this package was formerly part of PhyloNetworks v0.16.4 (and prior). PhyloNetworks v0.17, 1.0 (and later) are stripped of functions for trait evolution.

Owner

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

Citation (CITATION.bib) 

% reference for the software itself
@misc{PhyloTraits.jl,
	author  = {Cecile Ane <cecileane@users.noreply.github.com>, Paul Bastide <pbastide@users.noreply.github.com>, and contributors},
	title   = {PhyloTraits.jl},
	url     = {https://github.com/JuliaPhylo/PhyloTraits.jl},
	version = {v1.0.0},
	year    = {2025},
	month   = {7}
}
% paper on phylogenetic comparative methods for continuous traits on networks
@article{2018Bastide_continuoustraitevolution,
  author = {Bastide, Paul and Sol{\'\i}s-Lemus, Claudia and Kriebel, Ricardo and William Sparks, K and An{\'e}, C{\'e}cile},
  title = {Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations},
  journal = {Systematic Biology},
  year = {2018},
  volume = {67},
  number = {5},
  pages = {800-820},
  doi = {10.1093/sysbio/syy033},
}
% paper on phylogenetic comparative methods for discrete traits on networks
@article{2020Karimi_baobab_discretetraitevolution,
  author = {Karimi, Nisa and Grover, Corrinne E and Gallagher, Joseph P and Wendel, Jonathan F and An{\'e}, C{\'e}cile and Baum, David A},
  title = {Reticulate Evolution Helps Explain Apparent Homoplasy in Floral Biology and Pollination in Baobabs (\textit{{Adansonia}}; {Bombacoideae}; {Malvaceae})},
  journal = {Systematic Biology},
  year = {2020},
  volume = {69},
  number = {3},
  pages = {462-478},
  doi = {10.1093/sysbio/syz073},
}
% paper on continuous traits with intraspecific variation
@article{2023Teo_intraspeciesvariation,
  author = {Teo, Benjamin and Rose, Jeffrey P. and Bastide, Paul and An{\'e}, C{\'e}cile},
  title = {Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny},
  journal = {Bulletin of the Society of Systematic Biologists},
  year = {2023},
  volume = {2},
  number = {3},
  pages = {1-29},
  doi = {10.18061/bssb.v2i3.8977},
}

GitHub Events

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  • Issues event: 4
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  • Push event: 92
  • Pull request review event: 5
  • Pull request event: 7
Last Year
  • Create event: 5
  • Commit comment event: 4
  • Release event: 2
  • Issues event: 4
  • Watch event: 4
  • Delete event: 3
  • Issue comment event: 39
  • Push event: 92
  • Pull request review event: 5
  • Pull request event: 7

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 4
  • Average time to close issues: 1 day
  • Average time to close pull requests: 9 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 1.5
  • Average comments per pull request: 9.75
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 2
  • Pull requests: 4
  • Average time to close issues: 1 day
  • Average time to close pull requests: 9 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 1.5
  • Average comments per pull request: 9.75
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • benrkarin (1)
  • JuliaTagBot (1)
Pull Request Authors
  • cecileane (2)
  • jjustison (1)
  • dependabot[bot] (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • julia 4 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
juliahub.com: PhyloTraits

Julia package for the analysis of trait evolution along a phylogeny, including phylogenetic networks.

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4 Total
Rankings
Dependent repos count: 3.2%
Downloads: 4.4%
Average: 8.0%
Dependent packages count: 16.3%
Last synced: 10 months ago

Dependencies

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