PhyloNetworks
PhyloNetworks: a julia package with utilities for phylogenetic networks
Science Score: 67.0%
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✓DOI references
Found 4 DOI reference(s) in README -
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9 of 31 committers (29.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary
Keywords from Contributors
Repository
PhyloNetworks: a julia package with utilities for phylogenetic networks
Basic Info
Statistics
- Stars: 167
- Watchers: 16
- Forks: 50
- Open Issues: 8
- Releases: 28
Metadata Files
README.md
Overview
PhyloNetworks is a Julia package with utilities to to handle phylogenetic trees and networks. It serves as a core package that other packages can depend on, such as PhyloPlots to visualize phylogenies, SNaQ to infer phylogenies from genetic data, PhyloTraits to analyze the evolution of traits along phylogenies.
Phylogenetic networks represent the evolutionary relationships between a set of organisms, e.g. populations, species, languages, cultures etc. They are also called admixture graphs when their leaves are populations of the same or closely related species. They are explicit graph representations, in which nodes represent ancestral populations / species, and edge lengths represent evolutionary time.
Utilities in this core package include: - read / write phylogenies in (extended) Newick format - manipulate networks: re-root, prune taxa, remove hybrid edges, transform a network with a semidirected nearest-neighbor interchange (sNNI), extract the major tree from a network, extract displayed networks / trees - compare networks with dissimilarity measures (e.g. the Robinson-Foulds distance on trees) - summarize samples of networks with support for local features (edges and clades of hybrid origin or sister to a hybrid clade) - fit edges lengths from average pairwise distances between leaves, using least-squares - network traversal routines
To get help, check
- the latest documentation
- PhyloUtilities: website for a step-by-step tutorial with background on networks, and associated scripts
- tutorial for comparative methods, including network calibration. (See this older 2023 workshop for a version using the older version 0.16 of PhyloNetworks.)
- the google group for common questions. Join the group to post/email your questions, or to receive information on new versions, bugs fixed, etc.
If you use the package, please cite (bibtex format here). For the PhyloNetworks package in particular, please cite:
- Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution 34(12):3292–3298. doi:10.1093/molbev/msx235
[!NOTE] Version 0.17 of PhyloNetworks is a major change from version v0.16.4. Many functionalities were moved to other packages (e.g. SNaQ.jl and PhyloTraits.jl), the names of many methods were changed, and various internal functions were improved with breaking changes (e.g. traversal routines). PhyloNetworks v0.17 should serve as a better "core", used by other packages with more specialized functionalities.
Owner
- Name: JuliaPhylo
- Login: JuliaPhylo
- Kind: organization
- Repositories: 1
- Profile: https://github.com/JuliaPhylo
Citation (CITATION.bib)
% reference for the software itself
@article{2017SolislemusBastideAne_PhyloNetworks,
author = {Sol{\'\i}s-Lemus, Claudia and Bastide, Paul and An{\'e}, C{\'e}cile},
title = {PhyloNetworks: A Package for Phylogenetic Networks},
journal = {Molecular Biology and Evolution},
year = {2017},
volume = {34},
number = {12},
pages = {3292-3298},
doi = {10.1093/molbev/msx235},
}
% paper describing network calibration, based on genetic distances estimated from gene trees
@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},
}
% dissertation describing semidirected NNI (nearest neighbor interchange)
% to modify a semidirected network: in Chapter 4
@phdthesis{2020AllenSavietta-Ane,
author = {Allen-Savietta, Cora},
title = {Estimating Phylogenetic Networks from Concatenated Sequence Alignments},
school = {The University of Wisconsin - Madison},
year = 2020,
note = {Ph.D. dissertation, advised by Cécile Ané, ProQuest Dissertations & Theses 28263540},
url = {https://www.proquest.com/docview/2476856270/},
pages = 165,
}
GitHub Events
Total
- Create event: 11
- Commit comment event: 7
- Issues event: 9
- Release event: 3
- Watch event: 11
- Delete event: 10
- Member event: 1
- Issue comment event: 28
- Push event: 231
- Pull request review comment event: 9
- Gollum event: 16
- Pull request event: 18
- Pull request review event: 18
Last Year
- Create event: 11
- Commit comment event: 7
- Issues event: 9
- Release event: 3
- Watch event: 11
- Delete event: 10
- Member event: 1
- Issue comment event: 28
- Push event: 231
- Pull request review comment event: 9
- Gollum event: 16
- Pull request event: 18
- Pull request review event: 18
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Claudia Solis-Lemus | c****s@g****m | 617 |
| Paul Bastide | p****e@g****m | 217 |
| Cecile Ane | c****e | 151 |
| Cecile Ane | c****e@w****u | 137 |
| John Spaw | j****w@m****u | 62 |
| William Sparks | k****s@w****u | 41 |
| Claudia Solis Lemus | c****a@s****u | 19 |
| github-actions[bot] | 4****] | 17 |
| crsl4 | c****4 | 17 |
| Cecile Ane | a****e@s****u | 16 |
| Christian Borst | C****t@g****m | 11 |
| Cora Allen-Savietta | 6****a | 6 |
| Cora Allen-Coleman | 6****n | 6 |
| celinescornavacca | c****a@c****l | 4 |
| Douglas Bates | d****s@g****m | 4 |
| ClaudiaSL | s****s@w****u | 3 |
| Tony Kelman | t****y@k****t | 3 |
| Christian Borst | c****t@g****m | 2 |
| Jingcheng Xu | 5****i | 2 |
| Eric Davies | i****2@g****m | 1 |
| Elliot Saba | s****t@g****m | 1 |
| bstkj | t****i@g****m | 1 |
| Julia TagBot | 5****t | 1 |
| Ruoyi Cai | R****5 | 1 |
| gabehassler | 3****r | 1 |
| Paul Bastide | p****e@m****g | 1 |
| Nathan Kolbow | n****w@w****u | 1 |
| JohnPSpaw | j****w@g****m | 1 |
| Gustavo A. Ballen | g****h@g****m | 1 |
| Claudia Solis Lemus | c****a@d****u | 1 |
| and 1 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 7
- Average time to close issues: about 1 month
- Average time to close pull requests: 6 days
- Total issue authors: 5
- Total pull request authors: 5
- Average comments per issue: 1.2
- Average comments per pull request: 0.57
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 5
- Pull requests: 7
- Average time to close issues: about 1 month
- Average time to close pull requests: 6 days
- Issue authors: 5
- Pull request authors: 5
- Average comments per issue: 1.2
- Average comments per pull request: 0.57
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- rain-zjg (1)
- sanjin725 (1)
- Wyclif3 (1)
- colbec (1)
- pablogarciamoro (1)
- alexfranzen (1)
- crsl4 (1)
Pull Request Authors
- cecileane (4)
- jjustison (3)
- NathanKolbow (2)
- ayusharma17 (1)
- cvigilv (1)
- dependabot[bot] (1)
- crsl4 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- julia 460 total
- Total dependent packages: 7
- Total dependent repositories: 0
- Total versions: 23
juliahub.com: PhyloNetworks
PhyloNetworks: a julia package with utilities for phylogenetic networks
- Documentation: https://docs.juliahub.com/General/PhyloNetworks/stable/
- License: MIT
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Latest release: 1.2.0
published 7 months ago
Rankings
Dependencies
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- actions/cache v1 composite
- actions/checkout v2 composite
- codecov/codecov-action v2 composite
- julia-actions/julia-buildpkg v1 composite
- julia-actions/julia-processcoverage v1 composite
- julia-actions/julia-runtest v1 composite
- julia-actions/setup-julia v1 composite
- r-lib/actions/setup-r v2 composite
- actions/checkout v2 composite
- BenchmarkTools 0.2
- Logging *
- PkgBenchmark 0.2