├── .gitignore ├── .gitlab-ci.yml ├── .readthedocs.yml ├── .travis.yml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── PTS ├── README.md ├── data │ ├── BigTestData.str.tar.xz │ ├── Reduced_dataset.structure │ ├── extraparams │ └── mainparams ├── fastStructure │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure_threader-faststructure │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure_threader-structure │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure_threader-structure_1 │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure_threader-structure_16 │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure_threader-structure_2 │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure_threader-structure_4 │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── structure_threader-structure_6 │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml └── structure_threader-structure_8 │ ├── downloads.xml │ ├── install.sh │ ├── results-definition.xml │ └── test-definition.xml ├── README.md ├── TestData ├── BigTestData.str.tar.xz ├── README.md ├── SmallTestData.structure ├── extraparams ├── indfile.txt ├── joblist.txt ├── mainparams ├── mav_benchmark_parameters.txt └── parameters.txt ├── benchmarks ├── ParallelStructure_runner.R ├── README.md ├── Side_by_side.png ├── Side_by_side.svg ├── bar_plotter.py ├── benchmark.sh ├── benchmark_fast.sh ├── speedup_plotter.py └── system_speedup_plotter.py ├── docs ├── benchmark.md ├── binaries.md ├── citation.md ├── external.md ├── faq.md ├── future.md ├── index.md ├── install.md ├── output.md ├── requirements.txt ├── test_data.md └── usage.md ├── helper_scripts ├── Dockerfile ├── README.md ├── install_faststructure.sh ├── install_maverick.sh ├── install_structure.sh └── structure.spec ├── mkdocs.yml ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py ├── structure_threader ├── __init__.py ├── argparser.py ├── bins │ ├── __init__.py │ ├── linux │ │ ├── MavericK │ │ ├── __init__.py │ │ ├── fastStructure │ │ └── structure │ └── osx │ │ ├── MavericK │ │ ├── fastStructure │ │ └── structure ├── colorer │ ├── __init__.py │ └── colorer.py ├── evanno │ ├── LICENSE │ ├── __init__.py │ ├── fastChooseK.py │ ├── harvesterCore.py │ └── structureHarvester.py ├── plotter │ ├── __init__.py │ ├── html_template.py │ └── structplot.py ├── sanity_checks │ ├── __init__.py │ └── sanity.py ├── skeletons │ ├── __init__.py │ └── stparams.py ├── structure_threader.py └── wrappers │ ├── __init__.py │ ├── alstructure_wrapper.R │ ├── alstructure_wrapper.py │ ├── faststructure_wrapper.py │ ├── maverick_wrapper.py │ └── structure_wrapper.py └── tests ├── alstructure_field_tests.sh ├── alstructure_function_tests.py ├── conftest.py ├── evanno_tests.py ├── fastStructure_field_test.sh ├── faststructure_function_tests.py ├── files ├── chooseK.txt ├── fS_run_K.1.log ├── fS_run_K.1.meanP ├── fS_run_K.1.meanQ ├── fS_run_K.2.log ├── fS_run_K.2.meanP ├── fS_run_K.2.meanQ ├── fS_run_K.3.log ├── fS_run_K.3.meanP ├── fS_run_K.3.meanQ ├── fS_run_K.4.log ├── fS_run_K.4.meanP ├── fS_run_K.4.meanQ ├── fS_run_K.5.log ├── fS_run_K.5.meanP ├── fS_run_K.5.meanQ ├── fS_run_K.6.log ├── fS_run_K.6.meanP ├── fS_run_K.6.meanQ ├── mav_K1 │ ├── outputEvidence.csv │ ├── outputEvidenceDetails.csv │ ├── outputEvidenceNormalised.csv │ ├── outputLikelihood.csv │ ├── outputLog.txt │ ├── outputQmatrixError_ind_K1.csv │ ├── outputQmatrixError_pop_K1.csv │ ├── outputQmatrix_gene_K1.csv │ ├── outputQmatrix_ind_K1.csv │ └── outputQmatrix_pop_K1.csv ├── mav_K2 │ ├── outputEvidence.csv │ ├── outputEvidenceDetails.csv │ ├── outputEvidenceNormalised.csv │ ├── outputLikelihood.csv │ ├── outputLog.txt │ ├── outputQmatrixError_ind_K2.csv │ ├── outputQmatrixError_pop_K2.csv │ ├── outputQmatrix_gene_K2.csv │ ├── outputQmatrix_ind_K2.csv │ └── outputQmatrix_pop_K2.csv ├── mav_K3 │ ├── outputEvidence.csv │ ├── outputEvidenceDetails.csv │ ├── outputEvidenceNormalised.csv │ ├── outputLikelihood.csv │ ├── outputLog.txt │ ├── outputQmatrixError_ind_K3.csv │ ├── outputQmatrixError_pop_K3.csv │ ├── outputQmatrix_gene_K3.csv │ ├── outputQmatrix_ind_K3.csv │ └── outputQmatrix_pop_K3.csv └── test_merged │ ├── outputEvidence.csv │ └── outputEvidenceDetails.csv ├── maverick_field_test.sh ├── maverick_functions_tests.py ├── mockups.py ├── sanity_tests.py ├── smalldata ├── BigTestData.bed.tar.xz ├── BigTestData.str.tar.xz ├── BigTestData.vcf.tar.xz ├── Reduced_dataset.structure ├── SmallTestData.vcf ├── 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