SNaQ
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
Science Score: 67.0%
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✓DOI references
Found 6 DOI reference(s) in README -
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Low similarity (13.1%) to scientific vocabulary
Keywords
Repository
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
Basic Info
Statistics
- Stars: 3
- Watchers: 4
- Forks: 1
- Open Issues: 14
- Releases: 1
Topics
Metadata Files
README.md
SNaQ: Maximum pseudolikelihood estimation of species network 
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Overview
SNaQ implements the statistical inference method in Solís-Lemus and Ané (2016). The procedure involves a numerical optimization of branch lengths and inheritance probabilities, and a heuristic search in the space of level-1 phylogenetic networks.
To get help, check
- the latest SNaQ documentation
- the latest PhyloNetworks documentation
- PhyloUtilities with a step-by-step tutorial from multi-locus sequences to necessary input for SNaQ
- tutorial for SNaQ estimation (from a 2023 workshop)
- the JuliaPhylo google group for common questions. Join the group to post/email your questions, or to receive information on new versions, bugs fixed, etc.
- search for answers in github issues and post a new issue to post a question or a report potential bugs.
Citing
For the SNaQ method in particular, please cite - Claudia Solís-Lemus and Cécile Ané (2016). Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. PLoS Genet 12(3):e1005896. doi:10.1371/journal.pgen.1005896
For the PhyloNetworks package, 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
See CITATION.bib for the relevant reference(s).
[!NOTE] Much of this package was formerly part of PhyloNetworks v0.16.4 (and prior). PhyloNetworks v0.17, v1.0 and later have been stripped of functions implementing the SNaQ method.
Owner
- Name: JuliaPhylo
- Login: JuliaPhylo
- Kind: organization
- Repositories: 1
- Profile: https://github.com/JuliaPhylo
Citation (CITATION.bib)
% reference for the software itself
@misc{SNaQ.jl,
author = {Claudia Sol{\'\i}s-Lemus <crsl4@users.noreply.github.com>, C{\'e}cile An{\'e} <cecileane@users.noreply.github.com>, and contributors},
title = {SNaQ.jl},
url = {https://github.com/JuliaPhylo/SNaQ.jl},
version = {v1.0.0},
year = {2025},
}
% reference for core dependency PhyloNetworks.jl
@article{PhyloNetworks.jl,
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 on the SNaQ method
@article{2016SolislemusAne_SNaQ,
author = {Sol{\'\i}s-Lemus, Claudia and An{\'e}, C{\'e}cile},
title = {Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting},
journal = {PLOS Genetics},
year = {2016},
volume = {12},
number = {3},
pages = {1-21},
doi = {10.1371/journal.pgen.1005896},
}
GitHub Events
Total
- Fork event: 2
- Create event: 7
- Commit comment event: 10
- Release event: 1
- Issues event: 8
- Watch event: 4
- Delete event: 2
- Issue comment event: 27
- Member event: 1
- Push event: 218
- Pull request review event: 21
- Pull request review comment event: 20
- Pull request event: 9
Last Year
- Fork event: 2
- Create event: 7
- Commit comment event: 10
- Release event: 1
- Issues event: 8
- Watch event: 4
- Delete event: 2
- Issue comment event: 27
- Member event: 1
- Push event: 218
- Pull request review event: 21
- Pull request review comment event: 20
- Pull request event: 9
Packages
- Total packages: 1
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Total downloads:
- julia 29 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
juliahub.com: SNaQ
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
- Documentation: https://docs.juliahub.com/General/SNaQ/stable/
- License: MIT
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Latest release: 1.0.0
published 10 months ago
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- julia-actions/julia-processcoverage v1 composite
- julia-actions/julia-runtest v1 composite
- julia-actions/setup-julia v2 composite
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