tracts 2.0 documentation
tracts is a Python library used to model migration histories based on ancestry
tracts in admixed individuals. Time-dependent gene flow from multiple populations
can be modeled. In tracts 2.0, sex-biased migration and recombination rates are
supported, enabling modeling and inference for both autosomes and the X chromosome.
Installing tracts
To install:
Clone the repository.
Open a terminal inside your local copy.
Run
pip install .
You can now import tracts as a Python package.
tracts is currently not distributed on PyPI or Conda.
Using tracts
For detailed guidelines on how to use tracts in practice, see the
README file in the GitHub repository.
Contents:
- tracts
- tracts
- tracts.chromosome
- tracts.core
- tracts.demography
- tracts.driver
get_time_scaled_model_bounds()get_time_scaled_model_func()load_driver_file()load_model_from_driver()load_population()locate_file_path()output_simulation_data()output_simulation_data_sex_biased()parse_chromosomes()parse_individual_filenames()parse_start_params()randomize()run_model()run_model_multi_init()run_model_sex_biased()run_tracts()scale_select_indices()
- tracts.haploid
- tracts.hybrid_pedigree
- tracts.indiv
- tracts.legacy
ChromChropairCompositeDemographicModelDemographicModelHaploidIndivPopulationTracteprint()optimize()optimize_bfgs()optimize_brute_fracs2()optimize_brute_multifracs()optimize_cob()optimize_cob_fracs()optimize_cob_fracs2()optimize_cob_multifracs()optimize_slsqp()plotmig()test_model_func()
- tracts.legacy_models
- tracts.logs
- tracts.phase_type_distribution
- tracts.population
- tracts.tract
- tracts.util
- tracts