├── .flake8 ├── .gitignore ├── .pre-commit-config.yaml ├── .prettierrc ├── CONTRIBUTING.md ├── INSTALL.md ├── LICENSE ├── README.md ├── pyproject.toml ├── scripts ├── __init__.py ├── compute_iso_point.py ├── convert_fasta2phylip.py ├── extract_col_from_seq.py ├── extract_domain_transition.py ├── extract_full_sequences.py ├── extract_proba_from_rst.py ├── extract_seq_prob.py ├── extract_seq_prob_v2.py ├── extract_sequences.py ├── get_position_cds_trimal.py ├── get_position_in_aln.py ├── map_on_tree.py ├── move_target_sequence_to_top.py ├── ms_comparative_analysis.py ├── ms_extract_phosphosite_information.py ├── ms_extract_phosphosites_from_mztab.py ├── ms_visualisation.py ├── parse_rst.py ├── parse_taxbrowser.py ├── plot_dnds_per_site.py ├── realign_nuc_on_aa.py ├── remove_empty_col.py ├── remove_ensembl_name_in_tree.py ├── rfd_convert_fasta_to_pir.py ├── rfd_extract_motif.py └── translate_dna.py └── tutorials ├── __init__.py ├── ancestral_sequences_reconstruction ├── asr.md ├── control_file.ctl └── wag.dat ├── fdr_qvalue.md ├── generative-protein-design-workshop ├── 01-structure-generation │ ├── README.md │ └── utils │ │ ├── analyse_structures.py │ │ └── select_best_design.py ├── 02-sequence-design │ ├── README.md │ └── utils │ │ ├── analyse_sequences.py │ │ ├── prepare_scaffold.py │ │ ├── select_sequences.py │ │ └── validate_design.py ├── 03-atomic-modelling │ ├── README.md │ └── utils │ │ ├── analyse_models.py │ │ ├── build_model.py │ │ ├── export_results.py │ │ ├── prepare_inputs.py │ │ └── validate_best_model.py ├── 04-summary │ └── README.md └── README.md ├── identification_phosposites ├── README.md └── data │ └── search_params.xml ├── ncbi_taxonomy.md ├── pervasive_selection_site_models ├── 1UVQ.pdb ├── 1UVQ_positive_sites.png ├── HLA_DQB1.cds.fasta ├── HLA_DQB1.nh ├── HLA_DQB1.tree ├── HLA_DQB1_M0M1M2M3M7M8.ctl ├── HLA_DQB1_M0M1M2M3M7M8.mlc ├── HLA_DQB1_M0M1M2M3M7M8.rst.txt ├── HLA_DQB1_M8a.ctl ├── HLA_DQB1_M8a.mlc ├── HLA_DQB1_gene_tree.nh ├── HLA_DQB1_names.txt ├── HLA_DQB1_subset.aa.fasta ├── HLA_DQB1_subset.aa.mafft.fasta ├── HLA_DQB1_subset.cds.fasta ├── HLA_DQB1_subset.cds.mafft.fasta ├── HLA_DQB1_subset.cds.mafft.trimal.cols ├── HLA_DQB1_subset.cds.mafft.trimal.fasta ├── HLA_DQB1_subset.cds.mafft.trimal.html ├── HLA_DQB1_subset.cds.mafft.trimal.phy ├── HLA_DQB1_subset.tree ├── Human_HLA_DQB1_orthologues.fa ├── README.md ├── beb.png ├── beb2.png ├── beb_python.png ├── id.list └── test.txt ├── positive_selection ├── 1UVQ.pdb ├── TF105351.Eut.3.53876.ctl ├── TF105351.Eut.3.53876.fixed.ctl ├── TF105351.Eut.3.53876.tree ├── TF105351.Eut.3.phy ├── branch_site.md ├── id.list ├── id2.list ├── site_selection.md ├── tf105351.eut.3.aln.png └── tree.png ├── protein_design ├── __init__.py └── improve_protein_protein_affinity │ ├── 8GZ5_Repair_SB30L_NB54R_YB109W_mutations.jpg │ ├── Makefile │ ├── README.md │ ├── __init__.py │ └── scripts │ ├── __init__.py │ ├── analyse_multivariants.py │ ├── download_pdb.py │ ├── extract_interface.py │ ├── foldx_wrapper.py │ ├── generate_multimutant_commands_file.py │ ├── generate_pssm_commands_file.py │ ├── parse_pssm_output.py │ ├── plot_pssm_heatmap.py │ ├── run_foldx_analysecomplex.py │ ├── run_foldx_repair.py │ └── utils.py ├── stability_impact ├── 4TVF.pdb ├── 4TVF_L280.png ├── README.md ├── foldx3.md └── foldx4.md └── test ├── 1UVQ.pdb ├── 2NG.dN ├── 2NG.dS ├── 2NG.t ├── 4fold.nuc ├── HLA_DQB1.cds.fasta ├── HLA_DQB1.nh ├── HLA_DQB1.tree ├── HLA_DQB1_M0M1M2M3M7M8.ctl ├── HLA_DQB1_M0M1M2M3M7M8.mlc ├── HLA_DQB1_M0M1M2M3M7M8.rst.txt ├── HLA_DQB1_M8a.ctl ├── HLA_DQB1_M8a.mlc ├── HLA_DQB1_gene_tree.nh ├── HLA_DQB1_names.txt ├── HLA_DQB1_subset.aa.fasta ├── HLA_DQB1_subset.aa.mafft.fasta ├── HLA_DQB1_subset.cds.fasta ├── HLA_DQB1_subset.cds.mafft.fasta ├── HLA_DQB1_subset.cds.mafft.fasta.bak001 ├── HLA_DQB1_subset.cds.mafft.trimal.cols ├── HLA_DQB1_subset.cds.mafft.trimal.fasta ├── HLA_DQB1_subset.cds.mafft.trimal.html ├── HLA_DQB1_subset.cds.mafft.trimal.phy 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