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Citation

How to cite

Please cite the following paper when using ipcoal:

  • McKenzie PF, Eaton DAR. ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network. Bioinformatics. 2020 Aug 15;36(14):4193-4196. doi: 10.1093/bioinformatics/btaa486 PMID: 32399564.

If you use ipcoal to perform coalescent simulations please also cite the following:

  • Baumdicker, Franz, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P Ragsdale, Georgia Tsambos, Sha Zhu, et al. 2022. “Efficient Ancestry and Mutation Simulation with Msprime 1.0.” Genetics 220 (3): iyab229. https://doi.org/10.1093/genetics/iyab229.

Bibtex

These references are also available in bibtex format below. 

@article{mckenzie_ipcoal_2020,
    title = {ipcoal: an interactive {Python} package for simulating and analyzing genealogies and sequences on a species tree or network},
    shorttitle = {ipcoal},
    url = {https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btaa486/5836496},
    doi = {10.1093/bioinformatics/btaa486},
    language = {en},
    urldate = {2020-07-14},
    journal = {Bioinformatics},
    author = {McKenzie, Patrick F. and Eaton, Deren A. R.},
    year = {2020},
}

@article{baumdicker_efficient_2022,
    title = {Efficient ancestry and mutation simulation with msprime 1.0},
    volume = {220},
    issn = {1943-2631},
    url = {https://doi.org/10.1093/genetics/iyab229},
    doi = {10.1093/genetics/iyab229},
    abstract = {Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.},
    number = {3},
    urldate = {2022-05-06},
    journal = {Genetics},
    author = {Baumdicker, Franz and Bisschop, Gertjan and Goldstein, Daniel and Gower, Graham and Ragsdale, Aaron P and Tsambos, Georgia and Zhu, Sha and Eldon, Bjarki and Ellerman, E Castedo and Galloway, Jared G and Gladstein, Ariella L and Gorjanc, Gregor and Guo, Bing and Jeffery, Ben and Kretzschumar, Warren W and Lohse, Konrad and Matschiner, Michael and Nelson, Dominic and Pope, Nathaniel S and Quinto-Cortés, Consuelo D and Rodrigues, Murillo F and Saunack, Kumar and Sellinger, Thibaut and Thornton, Kevin and van Kemenade, Hugo and Wohns, Anthony W and Wong, Yan and Gravel, Simon and Kern, Andrew D and Koskela, Jere and Ralph, Peter L and Kelleher, Jerome},
    month = mar,
    year = {2022},
    pages = {iyab229},
    file = {Full Text PDF:/home/deren/Zotero/storage/AA8Y5CAC/Baumdicker et al. - 2022 - Efficient ancestry and mutation simulation with ms.pdf:application/pdf;Snapshot:/home/deren/Zotero/storage/CHWW2J2J/6460344.html:text/html},
}