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Welcome to ipcoal
ipcoal is a package for simulating and analyzing genealogies and sequences across genomes, with a focus on phylogenetic-scale analyses. ipcoal builds upon the powerful coalescent simulator msprime, but provides a different syntax and workflow for describing and visualizing complex demographic models (e.g., divergence times, effective population sizes, migration events), calling simulation functions, and summarizing or analyzing results. ipcoal includes many methods for downstream analysis of coalescent simulations, such as calculating likelihoods under the Kingman coalescent, multispecies coalescent, and sequentially Markov coalescent models, as well as implementing phylogenetic inference software on simulated sequences.
The ipcoal package is designed for use in jupyter-notebooks to encourage reproducible and shareable results. It is a powerful tool for posterior predictive data analysis, methods validation, for generating training data for machine learning, and as a teaching tool for learning the coalescent process in an interactive and visual environment.
Our goals
- Accessible: Easy to install and easy to use, with documentation and cookbooks.
- Reproducible: Designed for interactive use in Jupyter notebooks.
- Reliable: Tested on each build.
- Comprehensible: We provide simple methods to verify and visualize models.
- Didactic: We provide exercises for teaching in a classroom.
- Transparent: Read our code and make it your own.
Contact us
- Questions or Feature requests? Raise a ticket at the GitHub repo.