├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── bin ├── DisjointSet.py ├── TreeCluster.py ├── benchmark_escape.sh ├── benchmark_setup.sh ├── benchmark_subset.py ├── benchmark_sweep_binding.sh ├── benchmark_sweep_cov2rbd.sh ├── benchmark_sweep_expression.sh ├── benchmark_sweep_h1.sh ├── benchmark_sweep_h3.sh ├── benchmark_sweep_hiv.sh ├── cached_semantics.py ├── clustal2newick.py ├── cluster_purity.py ├── color_protein.py ├── combinatorial_fitness.py ├── conservation.sh ├── cov.py ├── cov_fasta.py ├── escape.py ├── escape_energy.py ├── fasta2nexus.py ├── fasta2phylip.py ├── fb_model.py ├── fb_semantics.py ├── fitness_energy.py ├── flu.py ├── headlines.py ├── hiv.py ├── hiv_pol.py ├── hmm.py ├── language_model.py ├── locations.py ├── make_null.py ├── mammals.py ├── mutation.py ├── newick_reformat.py ├── parse_headline_mods.py ├── parse_semantic_headlines.py ├── phylo.sh ├── phylo_cluster.sh ├── plot_cluster_purity.py ├── plot_escape_results.py ├── plot_fitness_results.py ├── plot_reinfection.py ├── plot_sweep.py ├── plot_variants.py ├── regional_escape.py ├── reinfection.py ├── transformer_layers.py └── utils.py ├── cov_fasta.md ├── examples ├── example_results.txt ├── example_target.fa └── example_wt.fa ├── models ├── cov.hdf5 ├── flu.hdf5 └── hiv.hdf5 ├── requirements.txt └── results ├── HZBB21_Postscript_v0.pdf ├── README.md ├── cov ├── semantics │ ├── analyze_semantics_cov2rbd_bilstm_512.txt │ └── analyze_semantics_cov_bilstm_512.txt └── structure │ ├── pdb_color_sarscov2_mean.pml │ └── spike_trimer.pdb ├── escape_results.txt ├── fitness_results.txt ├── flu ├── semantics │ ├── analyze_semantics_flu_h1_bilstm_512.txt │ └── analyze_semantics_flu_h3_bilstm_512.txt └── structure │ ├── h1_trimer.pdb │ ├── h3_trimer1.pdb │ ├── h3_trimer2.pdb │ ├── h3_trimer3.pdb │ ├── pdb_color_h1_mean.pml │ └── pdb_color_h3_mean.pml └── hiv ├── semantics └── analyze_semantics_hiv_bilstm_512.txt └── structure ├── env_trimer1.pdb ├── env_trimer2.pdb ├── env_trimer3.pdb └── pdb_color_env_mean.pml /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/README.md -------------------------------------------------------------------------------- /bin/DisjointSet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/DisjointSet.py -------------------------------------------------------------------------------- /bin/TreeCluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/TreeCluster.py -------------------------------------------------------------------------------- /bin/benchmark_escape.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_escape.sh -------------------------------------------------------------------------------- /bin/benchmark_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_setup.sh -------------------------------------------------------------------------------- /bin/benchmark_subset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_subset.py -------------------------------------------------------------------------------- /bin/benchmark_sweep_binding.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_sweep_binding.sh -------------------------------------------------------------------------------- /bin/benchmark_sweep_cov2rbd.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_sweep_cov2rbd.sh -------------------------------------------------------------------------------- /bin/benchmark_sweep_expression.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_sweep_expression.sh -------------------------------------------------------------------------------- /bin/benchmark_sweep_h1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_sweep_h1.sh -------------------------------------------------------------------------------- /bin/benchmark_sweep_h3.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_sweep_h3.sh -------------------------------------------------------------------------------- /bin/benchmark_sweep_hiv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/benchmark_sweep_hiv.sh -------------------------------------------------------------------------------- /bin/cached_semantics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/cached_semantics.py -------------------------------------------------------------------------------- /bin/clustal2newick.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/clustal2newick.py -------------------------------------------------------------------------------- /bin/cluster_purity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/cluster_purity.py -------------------------------------------------------------------------------- /bin/color_protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/color_protein.py -------------------------------------------------------------------------------- /bin/combinatorial_fitness.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/combinatorial_fitness.py -------------------------------------------------------------------------------- /bin/conservation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/conservation.sh -------------------------------------------------------------------------------- /bin/cov.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/cov.py -------------------------------------------------------------------------------- /bin/cov_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/cov_fasta.py -------------------------------------------------------------------------------- /bin/escape.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/escape.py -------------------------------------------------------------------------------- /bin/escape_energy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/escape_energy.py -------------------------------------------------------------------------------- /bin/fasta2nexus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/fasta2nexus.py -------------------------------------------------------------------------------- /bin/fasta2phylip.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/fasta2phylip.py -------------------------------------------------------------------------------- /bin/fb_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/fb_model.py -------------------------------------------------------------------------------- /bin/fb_semantics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/fb_semantics.py -------------------------------------------------------------------------------- /bin/fitness_energy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/fitness_energy.py -------------------------------------------------------------------------------- /bin/flu.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/flu.py -------------------------------------------------------------------------------- /bin/headlines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/headlines.py -------------------------------------------------------------------------------- /bin/hiv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/hiv.py -------------------------------------------------------------------------------- /bin/hiv_pol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/hiv_pol.py -------------------------------------------------------------------------------- /bin/hmm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/hmm.py -------------------------------------------------------------------------------- /bin/language_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/language_model.py -------------------------------------------------------------------------------- /bin/locations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/locations.py -------------------------------------------------------------------------------- /bin/make_null.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/make_null.py -------------------------------------------------------------------------------- /bin/mammals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/mammals.py -------------------------------------------------------------------------------- /bin/mutation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/mutation.py -------------------------------------------------------------------------------- /bin/newick_reformat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/newick_reformat.py -------------------------------------------------------------------------------- /bin/parse_headline_mods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/parse_headline_mods.py -------------------------------------------------------------------------------- /bin/parse_semantic_headlines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/parse_semantic_headlines.py -------------------------------------------------------------------------------- /bin/phylo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/phylo.sh -------------------------------------------------------------------------------- /bin/phylo_cluster.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/phylo_cluster.sh -------------------------------------------------------------------------------- /bin/plot_cluster_purity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/plot_cluster_purity.py -------------------------------------------------------------------------------- /bin/plot_escape_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/plot_escape_results.py -------------------------------------------------------------------------------- /bin/plot_fitness_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/plot_fitness_results.py -------------------------------------------------------------------------------- /bin/plot_reinfection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/plot_reinfection.py -------------------------------------------------------------------------------- /bin/plot_sweep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/plot_sweep.py -------------------------------------------------------------------------------- /bin/plot_variants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/plot_variants.py -------------------------------------------------------------------------------- /bin/regional_escape.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/regional_escape.py -------------------------------------------------------------------------------- /bin/reinfection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/reinfection.py -------------------------------------------------------------------------------- /bin/transformer_layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/transformer_layers.py -------------------------------------------------------------------------------- /bin/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/bin/utils.py -------------------------------------------------------------------------------- /cov_fasta.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/cov_fasta.md -------------------------------------------------------------------------------- /examples/example_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/examples/example_results.txt -------------------------------------------------------------------------------- /examples/example_target.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/examples/example_target.fa -------------------------------------------------------------------------------- /examples/example_wt.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/examples/example_wt.fa -------------------------------------------------------------------------------- /models/cov.hdf5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/models/cov.hdf5 -------------------------------------------------------------------------------- /models/flu.hdf5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/models/flu.hdf5 -------------------------------------------------------------------------------- /models/hiv.hdf5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/models/hiv.hdf5 -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/requirements.txt -------------------------------------------------------------------------------- /results/HZBB21_Postscript_v0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/HZBB21_Postscript_v0.pdf -------------------------------------------------------------------------------- /results/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/README.md -------------------------------------------------------------------------------- /results/cov/semantics/analyze_semantics_cov2rbd_bilstm_512.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/cov/semantics/analyze_semantics_cov2rbd_bilstm_512.txt -------------------------------------------------------------------------------- /results/cov/semantics/analyze_semantics_cov_bilstm_512.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/cov/semantics/analyze_semantics_cov_bilstm_512.txt -------------------------------------------------------------------------------- /results/cov/structure/pdb_color_sarscov2_mean.pml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/cov/structure/pdb_color_sarscov2_mean.pml -------------------------------------------------------------------------------- /results/cov/structure/spike_trimer.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/cov/structure/spike_trimer.pdb -------------------------------------------------------------------------------- /results/escape_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/escape_results.txt -------------------------------------------------------------------------------- /results/fitness_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/fitness_results.txt -------------------------------------------------------------------------------- /results/flu/semantics/analyze_semantics_flu_h1_bilstm_512.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/semantics/analyze_semantics_flu_h1_bilstm_512.txt -------------------------------------------------------------------------------- /results/flu/semantics/analyze_semantics_flu_h3_bilstm_512.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/semantics/analyze_semantics_flu_h3_bilstm_512.txt -------------------------------------------------------------------------------- /results/flu/structure/h1_trimer.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/structure/h1_trimer.pdb -------------------------------------------------------------------------------- /results/flu/structure/h3_trimer1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/structure/h3_trimer1.pdb -------------------------------------------------------------------------------- /results/flu/structure/h3_trimer2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/structure/h3_trimer2.pdb -------------------------------------------------------------------------------- /results/flu/structure/h3_trimer3.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/structure/h3_trimer3.pdb -------------------------------------------------------------------------------- /results/flu/structure/pdb_color_h1_mean.pml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/structure/pdb_color_h1_mean.pml -------------------------------------------------------------------------------- /results/flu/structure/pdb_color_h3_mean.pml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/flu/structure/pdb_color_h3_mean.pml -------------------------------------------------------------------------------- /results/hiv/semantics/analyze_semantics_hiv_bilstm_512.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/hiv/semantics/analyze_semantics_hiv_bilstm_512.txt -------------------------------------------------------------------------------- /results/hiv/structure/env_trimer1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/hiv/structure/env_trimer1.pdb -------------------------------------------------------------------------------- /results/hiv/structure/env_trimer2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/hiv/structure/env_trimer2.pdb -------------------------------------------------------------------------------- /results/hiv/structure/env_trimer3.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/hiv/structure/env_trimer3.pdb -------------------------------------------------------------------------------- /results/hiv/structure/pdb_color_env_mean.pml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brianhie/viral-mutation/HEAD/results/hiv/structure/pdb_color_env_mean.pml --------------------------------------------------------------------------------