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README.md

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This is the repository for the manuscript:

Kohanovski*, Pontz*, Vande Zande, Selmecki, Dahan, Pilpel, Yona, Ram (2024) Aneuploidy can be an evolutionary diversion on the path to adaptation. Molecular Biology and Evolution, DOI:10.1093/molbev/msae052.

  • equal contribution

Repository structure

  • ms folder contains the manuscript ms.pdf, and latex and other files that are needed to build it.
  • src/inference.py - inference the parameters of the model using pyabc. Different priors are available. run python inference.py for usage instructions.
  • src/inference-noaneuploidy.py - inference the parameters of the model with no aneuploidy
  • src/inference-neutralaneuploidy.py - inference the parameters of the model with neutral aneuploidy
  • src/models/singleLocus.model.py - the model that is used by the inference scripts
  • data/growth - contains growth curves data that is used in the inference scripts as a prior for fitness distributions
  • results/ - inference execution results. Are used by the notebooks. Every folder of inference contains not only the inference db file, but also the source code (copy-paste of inference and model codes that were used) and the params file that contain all the parameters that the source code was executed with.
  • src/notebooks/ - notebooks that are used to draw figures, calculate HDI, WAIC and so on.
  • ms/ms.tex contains reference for each notebook in comments for every figure and data that is generated by these notebooks.

License

All code in this repo is licensed under the CC-BY-SA 4.0 license.

The licenses of the versions of the manuscript and preprint appear on the respective websites.