.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/source/LEEME.md
docs/source/Tutorial.ipynb
docs/source/TutorialInstructions.md
docs/source/conf.py
docs/source/index.rst
docs/source/modules.rst
docs/source/pygor3.rst
docs/source/pygor3.scripts.rst
docs/source/pygor3_tutorial.rst
docs/source/readme_link.rst
docs/source/tutorial_2022.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/entropy.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/HIP00110.tsv.gz
pygor3/demo/notebooks/IGoR_diagram.png
pygor3/demo/notebooks/Killifish_D_genes.fasta
pygor3/demo/notebooks/Killifish_Genomic_template_modifications.ipynb
pygor3/demo/notebooks/Killifish_J_anchors.csv
pygor3/demo/notebooks/Killifish_J_genes.fasta
pygor3/demo/notebooks/Killifish_V_anchors.csv
pygor3/demo/notebooks/Killifish_V_genes.fasta
pygor3/demo/notebooks/Killifish_example.ipynb
pygor3/demo/notebooks/QuickStart.ipynb
pygor3/demo/notebooks/Testing.ipynb
pygor3/demo/notebooks/Tutorial.ipynb
pygor3/demo/notebooks/d00_Configuration.ipynb
pygor3/demo/notebooks/d01_RunIGoR.ipynb
pygor3/demo/notebooks/d02_ExploringModels.ipynb
pygor3/demo/notebooks/d03_EditModel.ipynb
pygor3/demo/notebooks/d04_InferringNewModel.ipynb
pygor3/demo/notebooks/d11_Observables_2.ipynb
pygor3/demo/notebooks/d12_Observables_3.ipynb
pygor3/demo/notebooks/.ipynb_checkpoints/Function_BestScenarios-checkpoint.ipynb
pygor3/demo/notebooks/.ipynb_checkpoints/Testing-checkpoint.ipynb
pygor3/demo/notebooks/.ipynb_checkpoints/Tutorial02-checkpoint.ipynb
pygor3/demo/notebooks/Killifish_genome_template/d.fasta
pygor3/demo/notebooks/Killifish_genome_template/d_no_imgt.fasta
pygor3/demo/notebooks/Killifish_genome_template/j.fasta
pygor3/demo/notebooks/Killifish_genome_template/j_no_imgt.fasta
pygor3/demo/notebooks/Killifish_genome_template/v.fasta
pygor3/demo/notebooks/Killifish_genome_template/v_no_imgt.fasta
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.bk
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_align.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