The ipcoal ethos

Welcome to ipcoal, a simple tool for simulating and analyzing genealogies and sequences across genomes in a phylogenetic context. ipcoal builds upon the powerful coalescent simulator msprime to automate the task of describing complex demographic models (e.g., divergence times, effective population sizes, migration events) when simulating the coalescent process on phylogenetic trees or networks.

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.
  • Comprehendable: We provide simple methods to verify and visualize models.
  • Didactic: We provide (binder) notebooks for teaching in a classroom.
  • Transparent: Read our code and make it your own.

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