.gitignore
.gitmodules
BayesNetwork.png
Dockerfile
GeneChoice_CP.png
GeneChoice_MP.png
LICENSE
README.md
dpygor
pyproject.toml
requirements.txt
schema.mdj
setup.py
test.py
PyIR/__init__.py
PyIR/setup.py
PyIR/pyir/__init__.py
PyIR/pyir/arg_parse.py
PyIR/pyir/factory.py
PyIR/pyir/filters.py
PyIR/pyir/igblast.py
PyIR/pyir/output.py
PyIR/pyir/parsers.py
docs/make.bat
docs/build/.buildinfo
docs/build/genindex.html
docs/build/index.html
docs/build/objects.inv
docs/build/pygor3_tutorial.html
docs/build/readme.html
docs/build/search.html
docs/build/searchindex.js
docs/build/.doctrees/environment.pickle
docs/build/.doctrees/index.doctree
docs/build/.doctrees/pygor3_tutorial.doctree
docs/build/.doctrees/readme.doctree
docs/build/_sources/index.rst.txt
docs/build/_sources/pygor3_tutorial.rst.txt
docs/build/_sources/readme.rst.txt
docs/build/_static/basic.css
docs/build/_static/doctools.js
docs/build/_static/documentation_options.js
docs/build/_static/file.png
docs/build/_static/jquery-3.5.1.js
docs/build/_static/jquery.js
docs/build/_static/language_data.js
docs/build/_static/minus.png
docs/build/_static/plus.png
docs/build/_static/pygments.css
docs/build/_static/searchtools.js
docs/build/_static/underscore-1.13.1.js
docs/build/_static/underscore.js
docs/build/_static/css/badge_only.css
docs/build/_static/css/theme.css
docs/build/_static/css/fonts/Roboto-Slab-Bold.woff
docs/build/_static/css/fonts/Roboto-Slab-Bold.woff2
docs/build/_static/css/fonts/Roboto-Slab-Regular.woff
docs/build/_static/css/fonts/Roboto-Slab-Regular.woff2
docs/build/_static/css/fonts/fontawesome-webfont.eot
docs/build/_static/css/fonts/fontawesome-webfont.svg
docs/build/_static/css/fonts/fontawesome-webfont.ttf
docs/build/_static/css/fonts/fontawesome-webfont.woff
docs/build/_static/css/fonts/fontawesome-webfont.woff2
docs/build/_static/css/fonts/lato-bold-italic.woff
docs/build/_static/css/fonts/lato-bold-italic.woff2
docs/build/_static/css/fonts/lato-bold.woff
docs/build/_static/css/fonts/lato-bold.woff2
docs/build/_static/css/fonts/lato-normal-italic.woff
docs/build/_static/css/fonts/lato-normal-italic.woff2
docs/build/_static/css/fonts/lato-normal.woff
docs/build/_static/css/fonts/lato-normal.woff2
docs/build/_static/fonts/Inconsolata-Bold.ttf
docs/build/_static/fonts/Inconsolata-Regular.ttf
docs/build/_static/fonts/Inconsolata.ttf
docs/build/_static/fonts/Lato-Bold.ttf
docs/build/_static/fonts/Lato-Regular.ttf
docs/build/_static/fonts/RobotoSlab-Bold.ttf
docs/build/_static/fonts/RobotoSlab-Regular.ttf
docs/build/_static/fonts/fontawesome-webfont.eot
docs/build/_static/fonts/fontawesome-webfont.svg
docs/build/_static/fonts/fontawesome-webfont.ttf
docs/build/_static/fonts/fontawesome-webfont.woff
docs/build/_static/fonts/fontawesome-webfont.woff2
docs/build/_static/fonts/Lato/lato-bold.eot
docs/build/_static/fonts/Lato/lato-bold.ttf
docs/build/_static/fonts/Lato/lato-bold.woff
docs/build/_static/fonts/Lato/lato-bold.woff2
docs/build/_static/fonts/Lato/lato-bolditalic.eot
docs/build/_static/fonts/Lato/lato-bolditalic.ttf
docs/build/_static/fonts/Lato/lato-bolditalic.woff
docs/build/_static/fonts/Lato/lato-bolditalic.woff2
docs/build/_static/fonts/Lato/lato-italic.eot
docs/build/_static/fonts/Lato/lato-italic.ttf
docs/build/_static/fonts/Lato/lato-italic.woff
docs/build/_static/fonts/Lato/lato-italic.woff2
docs/build/_static/fonts/Lato/lato-regular.eot
docs/build/_static/fonts/Lato/lato-regular.ttf
docs/build/_static/fonts/Lato/lato-regular.woff
docs/build/_static/fonts/Lato/lato-regular.woff2
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff
docs/build/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2
docs/build/_static/js/badge_only.js
docs/build/_static/js/html5shiv-printshiv.min.js
docs/build/_static/js/html5shiv.min.js
docs/build/_static/js/modernizr.min.js
docs/build/_static/js/theme.js
docs/build/doctrees/README.doctree
docs/build/doctrees/Tutorial.doctree
docs/build/doctrees/environment.pickle
docs/build/doctrees/index.doctree
docs/build/doctrees/pygor3_tutorial.doctree
docs/build/doctrees/pygor_tutorial.doctree
docs/build/doctrees/readme.doctree
docs/build/doctrees/nbsphinx/Tutorial.ipynb
docs/build/doctrees/nbsphinx/Tutorial_11_1.png
docs/build/doctrees/nbsphinx/Tutorial_12_1.png
docs/build/doctrees/nbsphinx/Tutorial_131_1.png
docs/build/doctrees/nbsphinx/Tutorial_135_1.png
docs/build/doctrees/nbsphinx/Tutorial_137_1.png
docs/build/doctrees/nbsphinx/Tutorial_138_1.png
docs/build/doctrees/nbsphinx/Tutorial_13_1.png
docs/build/doctrees/nbsphinx/Tutorial_15_1.png
docs/build/doctrees/nbsphinx/Tutorial_16_1.png
docs/build/doctrees/nbsphinx/Tutorial_17_1.png
docs/build/doctrees/nbsphinx/Tutorial_18_1.png
docs/build/doctrees/nbsphinx/Tutorial_19_1.png
docs/build/doctrees/nbsphinx/Tutorial_218_1.png
docs/build/doctrees/nbsphinx/Tutorial_21_1.png
docs/build/doctrees/nbsphinx/Tutorial_22_1.png
docs/build/doctrees/nbsphinx/Tutorial_23_1.png
docs/build/doctrees/nbsphinx/Tutorial_32_1.png
docs/build/doctrees/nbsphinx/Tutorial_33_1.png
docs/build/doctrees/nbsphinx/Tutorial_35_1.png
docs/build/doctrees/nbsphinx/Tutorial_37_1.png
docs/build/doctrees/nbsphinx/Tutorial_41_1.png
docs/build/doctrees/nbsphinx/Tutorial_43_1.png
docs/build/doctrees/nbsphinx/Tutorial_65_0.png
docs/build/doctrees/nbsphinx/Tutorial_65_1.png
docs/build/doctrees/nbsphinx/Tutorial_65_2.png
docs/build/doctrees/nbsphinx/Tutorial_65_3.png
docs/build/doctrees/nbsphinx/Tutorial_65_4.png
docs/build/doctrees/nbsphinx/Tutorial_65_5.png
docs/build/doctrees/nbsphinx/Tutorial_65_6.png
docs/build/doctrees/nbsphinx/Tutorial_65_7.png
docs/build/doctrees/nbsphinx/Tutorial_65_8.png
docs/build/doctrees/nbsphinx/Tutorial_65_9.png
docs/build/doctrees/nbsphinx/Tutorial_66_1.png
docs/build/doctrees/nbsphinx/Tutorial_71_0.png
docs/build/doctrees/nbsphinx/Tutorial_71_1.png
docs/build/doctrees/nbsphinx/Tutorial_71_2.png
docs/build/doctrees/nbsphinx/Tutorial_71_3.png
docs/build/doctrees/nbsphinx/Tutorial_71_4.png
docs/build/doctrees/nbsphinx/Tutorial_71_5.png
docs/build/doctrees/nbsphinx/Tutorial_71_6.png
docs/build/doctrees/nbsphinx/Tutorial_71_7.png
docs/build/doctrees/nbsphinx/Tutorial_71_8.png
docs/build/doctrees/nbsphinx/Tutorial_71_9.png
docs/build/doctrees/nbsphinx/Tutorial_72_1.png
docs/build/doctrees/nbsphinx/Tutorial_76_1.png
docs/build/doctrees/nbsphinx/Tutorial_77_1.png
docs/build/doctrees/nbsphinx/Tutorial_7_0.png
docs/build/doctrees/nbsphinx/Tutorial_7_1.png
docs/build/doctrees/nbsphinx/Tutorial_82_1.png
docs/build/doctrees/nbsphinx/Tutorial_83_1.png
docs/build/doctrees/nbsphinx/Tutorial_84_1.png
docs/build/doctrees/nbsphinx/Tutorial_89_1.png
docs/build/doctrees/nbsphinx/Tutorial_8_0.png
docs/build/doctrees/nbsphinx/Tutorial_8_1.png
docs/build/doctrees/nbsphinx/Tutorial_90_1.png
docs/build/html/.buildinfo
docs/build/html/Tutorial.html
docs/build/html/Tutorial.ipynb
docs/build/html/genindex.html
docs/build/html/index.html
docs/build/html/objects.inv
docs/build/html/py-modindex.html
docs/build/html/pygor3_tutorial.html
docs/build/html/pygor_tutorial.html
docs/build/html/readme.html
docs/build/html/search.html
docs/build/html/searchindex.js
docs/build/html/_images/Tutorial_11_1.png
docs/build/html/_images/Tutorial_12_1.png
docs/build/html/_images/Tutorial_131_1.png
docs/build/html/_images/Tutorial_135_1.png
docs/build/html/_images/Tutorial_137_1.png
docs/build/html/_images/Tutorial_138_1.png
docs/build/html/_images/Tutorial_13_1.png
docs/build/html/_images/Tutorial_15_1.png
docs/build/html/_images/Tutorial_16_1.png
docs/build/html/_images/Tutorial_17_1.png
docs/build/html/_images/Tutorial_18_1.png
docs/build/html/_images/Tutorial_19_1.png
docs/build/html/_images/Tutorial_218_1.png
docs/build/html/_images/Tutorial_21_1.png
docs/build/html/_images/Tutorial_22_1.png
docs/build/html/_images/Tutorial_23_1.png
docs/build/html/_images/Tutorial_32_1.png
docs/build/html/_images/Tutorial_33_1.png
docs/build/html/_images/Tutorial_35_1.png
docs/build/html/_images/Tutorial_37_1.png
docs/build/html/_images/Tutorial_41_1.png
docs/build/html/_images/Tutorial_43_1.png
docs/build/html/_images/Tutorial_65_0.png
docs/build/html/_images/Tutorial_65_1.png
docs/build/html/_images/Tutorial_65_2.png
docs/build/html/_images/Tutorial_65_3.png
docs/build/html/_images/Tutorial_65_4.png
docs/build/html/_images/Tutorial_65_5.png
docs/build/html/_images/Tutorial_65_6.png
docs/build/html/_images/Tutorial_65_7.png
docs/build/html/_images/Tutorial_65_8.png
docs/build/html/_images/Tutorial_65_9.png
docs/build/html/_images/Tutorial_66_1.png
docs/build/html/_images/Tutorial_71_0.png
docs/build/html/_images/Tutorial_71_1.png
docs/build/html/_images/Tutorial_71_2.png
docs/build/html/_images/Tutorial_71_3.png
docs/build/html/_images/Tutorial_71_4.png
docs/build/html/_images/Tutorial_71_5.png
docs/build/html/_images/Tutorial_71_6.png
docs/build/html/_images/Tutorial_71_7.png
docs/build/html/_images/Tutorial_71_8.png
docs/build/html/_images/Tutorial_71_9.png
docs/build/html/_images/Tutorial_72_1.png
docs/build/html/_images/Tutorial_76_1.png
docs/build/html/_images/Tutorial_77_1.png
docs/build/html/_images/Tutorial_7_0.png
docs/build/html/_images/Tutorial_7_1.png
docs/build/html/_images/Tutorial_82_1.png
docs/build/html/_images/Tutorial_83_1.png
docs/build/html/_images/Tutorial_84_1.png
docs/build/html/_images/Tutorial_89_1.png
docs/build/html/_images/Tutorial_8_0.png
docs/build/html/_images/Tutorial_8_1.png
docs/build/html/_images/Tutorial_90_1.png
docs/build/html/_sources/README.md.txt
docs/build/html/_sources/Tutorial.ipynb.txt
docs/build/html/_sources/index.rst.txt
docs/build/html/_sources/pygor3_tutorial.rst.txt
docs/build/html/_sources/pygor_tutorial.rst.txt
docs/build/html/_sources/readme.rst.txt
docs/build/html/_static/alabaster.css
docs/build/html/_static/basic.css
docs/build/html/_static/custom.css
docs/build/html/_static/doctools.js
docs/build/html/_static/documentation_options.js
docs/build/html/_static/file.png
docs/build/html/_static/jquery-3.5.1.js
docs/build/html/_static/jquery.js
docs/build/html/_static/language_data.js
docs/build/html/_static/minus.png
docs/build/html/_static/plus.png
docs/build/html/_static/pygments.css
docs/build/html/_static/searchtools.js
docs/build/html/_static/underscore-1.13.1.js
docs/build/html/_static/underscore.js
docs/build/html/_static/css/badge_only.css
docs/build/html/_static/css/theme.css
docs/build/html/_static/css/fonts/Roboto-Slab-Bold.woff
docs/build/html/_static/css/fonts/Roboto-Slab-Bold.woff2
docs/build/html/_static/css/fonts/Roboto-Slab-Regular.woff
docs/build/html/_static/css/fonts/Roboto-Slab-Regular.woff2
docs/build/html/_static/css/fonts/fontawesome-webfont.eot
docs/build/html/_static/css/fonts/fontawesome-webfont.svg
docs/build/html/_static/css/fonts/fontawesome-webfont.ttf
docs/build/html/_static/css/fonts/fontawesome-webfont.woff
docs/build/html/_static/css/fonts/fontawesome-webfont.woff2
docs/build/html/_static/css/fonts/lato-bold-italic.woff
docs/build/html/_static/css/fonts/lato-bold-italic.woff2
docs/build/html/_static/css/fonts/lato-bold.woff
docs/build/html/_static/css/fonts/lato-bold.woff2
docs/build/html/_static/css/fonts/lato-normal-italic.woff
docs/build/html/_static/css/fonts/lato-normal-italic.woff2
docs/build/html/_static/css/fonts/lato-normal.woff
docs/build/html/_static/css/fonts/lato-normal.woff2
docs/build/html/_static/fonts/Inconsolata-Bold.ttf
docs/build/html/_static/fonts/Inconsolata-Regular.ttf
docs/build/html/_static/fonts/Inconsolata.ttf
docs/build/html/_static/fonts/Lato-Bold.ttf
docs/build/html/_static/fonts/Lato-Regular.ttf
docs/build/html/_static/fonts/RobotoSlab-Bold.ttf
docs/build/html/_static/fonts/RobotoSlab-Regular.ttf
docs/build/html/_static/fonts/fontawesome-webfont.eot
docs/build/html/_static/fonts/fontawesome-webfont.svg
docs/build/html/_static/fonts/fontawesome-webfont.ttf
docs/build/html/_static/fonts/fontawesome-webfont.woff
docs/build/html/_static/fonts/fontawesome-webfont.woff2
docs/build/html/_static/fonts/Lato/lato-bold.eot
docs/build/html/_static/fonts/Lato/lato-bold.ttf
docs/build/html/_static/fonts/Lato/lato-bold.woff
docs/build/html/_static/fonts/Lato/lato-bold.woff2
docs/build/html/_static/fonts/Lato/lato-bolditalic.eot
docs/build/html/_static/fonts/Lato/lato-bolditalic.ttf
docs/build/html/_static/fonts/Lato/lato-bolditalic.woff
docs/build/html/_static/fonts/Lato/lato-bolditalic.woff2
docs/build/html/_static/fonts/Lato/lato-italic.eot
docs/build/html/_static/fonts/Lato/lato-italic.ttf
docs/build/html/_static/fonts/Lato/lato-italic.woff
docs/build/html/_static/fonts/Lato/lato-italic.woff2
docs/build/html/_static/fonts/Lato/lato-regular.eot
docs/build/html/_static/fonts/Lato/lato-regular.ttf
docs/build/html/_static/fonts/Lato/lato-regular.woff
docs/build/html/_static/fonts/Lato/lato-regular.woff2
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff
docs/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2
docs/build/html/_static/js/badge_only.js
docs/build/html/_static/js/html5shiv-printshiv.min.js
docs/build/html/_static/js/html5shiv.min.js
docs/build/html/_static/js/modernizr.min.js
docs/build/html/_static/js/theme.js
docs/source/Tutorial.ipynb
docs/source/best_scenarios_counts.csv
docs/source/conf.py
docs/source/index.rst
docs/source/pygor3_tutorial.rst
docs/source/readme.rst
pygor3/AIRR.py
pygor3/IgorBestScenarios.py
pygor3/IgorDB.sql
pygor3/IgorDBBestScenariosVDJ.sql
pygor3/IgorDefaults.py
pygor3/IgorDictionaries.py
pygor3/IgorIO.py
pygor3/IgorIndexedSequence.py
pygor3/IgorIndexedSequencesDB.py
pygor3/IgorSQL.py
pygor3/IgorSqliteDB.py
pygor3/IgorSqliteDBBestScenarios.py
pygor3/__init__.py
pygor3/config.json
pygor3/config.py
pygor3/imgt.py
pygor3/utils.py
pygor3/utils_pre_processing.py
pygor3.egg-info/PKG-INFO
pygor3.egg-info/SOURCES.txt
pygor3.egg-info/dependency_links.txt
pygor3.egg-info/entry_points.txt
pygor3.egg-info/requires.txt
pygor3.egg-info/top_level.txt
pygor3/demo/data/IgL/IgL_seqs_memory_Functional.txt
pygor3/demo/data/IgL/IgL_seqs_memory_Nofunctional.txt
pygor3/demo/data/IgL/IgL_seqs_naive_Functional.txt
pygor3/demo/data/IgL/IgL_seqs_naive_Functional_small.txt
pygor3/demo/data/IgL/IgL_seqs_naive_Nofunctional.txt
pygor3/demo/notebooks/Documentation.ipynb
pygor3/demo/notebooks/Function_BestScenarios.ipynb
pygor3/demo/notebooks/QuickStart.ipynb
pygor3/demo/notebooks/Testing.ipynb
pygor3/demo/notebooks/Tutorial.ipynb
pygor3/demo/notebooks/Tutorial02.ipynb
pygor3/demo/notebooks/Untitled1.ipynb
pygor3/demo/notebooks/Untitled3.ipynb
pygor3/demo/notebooks/Untitled5.ipynb
pygor3/demo/notebooks/d01_ExploringModels.ipynb
pygor3/demo/notebooks/d02_EditModel.ipynb
pygor3/demo/notebooks/d03_RunIGoR.ipynb
pygor3/demo/notebooks/d03_generate_seqs.py
pygor3/demo/notebooks/d04_BestScenarios.ipynb
pygor3/demo/notebooks/d05_Alignments.ipynb
pygor3/demo/notebooks/d07_CDR3_from_bs.ipynb
pygor3/demo/notebooks/d08_d-separation.ipynb
pygor3/demo/notebooks/d10_Observables.ipynb
pygor3/demo/notebooks/d11_Observables_2.ipynb
pygor3/demo/notebooks/don.txt
pygor3/demo/notebooks/don_ma.txt
pygor3/demo/notebooks/mdl_marginals0.txt
pygor3/demo/notebooks/mdl_marginals1.txt
pygor3/demo/notebooks/mdl_marginals3.txt
pygor3/demo/notebooks/mdl_parms0.txt
pygor3/demo/notebooks/mdl_parms1.txt
pygor3/demo/notebooks/mdl_parms3.txt
pygor3/demo/notebooks/.ipynb_checkpoints/Function_BestScenarios-checkpoint.ipynb
pygor3/demo/notebooks/.ipynb_checkpoints/Testing-checkpoint.ipynb
pygor3/demo/notebooks/.ipynb_checkpoints/Tutorial-checkpoint.ipynb
pygor3/demo/notebooks/.ipynb_checkpoints/Tutorial02-checkpoint.ipynb
pygor3/gui/p3example.py
pygor3/gui/p3example000.py
pygor3/gui/p3example002.py
pygor3/gui/pygor3_app.py
pygor3/gui/pygor3_app_events.py
pygor3/gui/pygor3_evaluate.py
pygor3/gui/pygor3_report.py
pygor3/gui/pygor3_run.py
pygor3/prepro/MixcrPreProcessPairedSeqs.py
pygor3/scripts/__init__.py
pygor3/scripts/all_gene_alignments_id.py
pygor3/scripts/bs_export.py
pygor3/scripts/bs_pairwise_prob.py
pygor3/scripts/cli.py
pygor3/scripts/download_imgt_gene_templates.py
pygor3/scripts/get_imgt_data.py
pygor3/scripts/infer_sequences.py
pygor3/scripts/load_database.py
pygor3/scripts/model_create.py
pygor3/scripts/model_export.py
pygor3/scripts/model_plot.py
pygor3/scripts/naive_align.py
pygor3/scripts/naive_align_id.py
pygor3/scripts/observable.py
pygor3/scripts/pgen_sequences.py
pygor3/scripts/plot_marginals.py
pygor3/scripts/scriptTest.py
pygor3/scripts/scriptTest02.py
pygor3/scripts/short_names_imgt_templates.py
pygor3/scripts/stas_from_bs.py
pygor3/unittests/test_IgorIO.py
pygor3/unittests/test_IgorModel.py
pygor3/unittests/test_IgorModel_Parms.py
pygor3/unittests/test_IgorRec_Event.py
pygor3/unittests/test_IgorRefGenome.py
pygor3/unittests/test_IgorSqliteDB.py
pygor3/unittests/test_IgorTask.py
pygor3/unittests/test_cli.py
pygor3/unittests/test_evaluate.py
pygor3/unittests/test_generate.py
pygor3/unittests/test_imgt.py
pygor3/unittests/test_infer.py
pygor3/unittests/test_observables.py
pygor3/unittests/test_plots.py
pygor3/unittests/test_pre_processing.py
pygor3/unittests/test_rcParams.py
pygor3/unittests/test_single_command.py
pygor3/unittests/test_utils.py