epistasis.simulate package

epistasis.simulate.base module

epistasis.simulate.linear module

class epistasis.simulate.linear.LinearSimulation(wildtype, mutations, model_type='global', **kwargs)

Bases: epistasis.simulate.base.BaseSimulation

Construct an genotype-phenotype from linear building blocks and epistatic coefficients.


Phenotype = b0 + b1 + b2 + b3 + b12 + b13 + b13 + b123

  • wildtype (str) – Wildtype genotype
  • mutations (dict) – Mapping for each site to its alphabet
  • order (int) – Order of epistasis in simulated genotype-phenotype map
  • betas (array-like) – values of epistatic coefficients (must be positive for this function to work. Log is taken)
  • model_type (str) – Use a local or global (i.e. Walsh space) epistasis model to construct phenotypes

Build the phenotype map from epistatic interactions.

epistasis.simulate.power module