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ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network

View ORCID ProfilePatrick F. McKenzie, View ORCID ProfileDeren A. R. Eaton
doi: https://doi.org/10.1101/2020.01.15.908236
Patrick F. McKenzie
Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
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  • For correspondence: p.mckenzie@columbia.edu
Deren A. R. Eaton
Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
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Abstract

Summary ipcoal is a free and open source Python package for simulating and analyzing genealogies and sequences. It automates the task of describing complex demographic models (e.g., with divergence times, effective population sizes, migration events) to the msprime coalescent simulator by parsing a user-supplied species tree or network. Genealogies, sequences, and metadata are returned in tabular format allowing for easy downstream analyses. ipcoal includes phylogenetic inference tools to automate gene tree inference from simulated sequence data, and visualization tools for analyzing results and verifying model accuracy. The ipcoal package is a powerful tool for posterior predictive data analysis, for methods validation, and for teaching coalescent methods in an interactive and visual environment.

Availability and implementation Source code is available from the GitHub repository (https://github.com/pmckenz1/ipcoal/) and is distributed for packaged installation with conda. Complete documentation and interactive notebooks prepared for teaching purposes are available at https://ipcoal.readthedocs.io/.

Footnotes

  • https://github.com/pmckenz1/ipcoal

  • https://ipcoal.readthedocs.io/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 16, 2020.
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ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
Patrick F. McKenzie, Deren A. R. Eaton
bioRxiv 2020.01.15.908236; doi: https://doi.org/10.1101/2020.01.15.908236
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ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
Patrick F. McKenzie, Deren A. R. Eaton
bioRxiv 2020.01.15.908236; doi: https://doi.org/10.1101/2020.01.15.908236

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