1. Install python
2. Install dependencies: pip install -r requirements.txt
3. Run the application: python main.py

Load a csv file containing the mutation rates: marker_set.read_marker_set_from_file(r"manuscript/mutationrates/1.csv")

Load a tgf file containing the pedigree: pedigree.read_pedigree_from_file("manuscript/basepedigreeA.tgf")

Load at least one csv file containing the known haplotypes of individuals present in your pedigree file: pedigree.read_known_haplotype_from_file("suspect", "manuscript/haplotypes/suspect.csv", marker_set) pedigree.read_known_haplotype_from_file("known1", "manuscript/haplotypes/known_plus1.csv", marker_set)

Set the suspect by entering the same identifyer that is used in the pedigree and known haplotype files: suspect = "suspect"

Set the simultation parameters (number of iterations): simulation = run_simulation(pedigree, marker_set, suspect, number_of_iterations=100000)