.gitignore
LICENSE.md
README.md
learnMSA.py
learnMSA_demo.ipynb
learnMSA_with_language_model_demo.ipynb
pyproject.toml
setup.py
learnMSA/__init__.py
learnMSA/_version.py
learnMSA.egg-info/PKG-INFO
learnMSA.egg-info/SOURCES.txt
learnMSA.egg-info/dependency_links.txt
learnMSA.egg-info/entry_points.txt
learnMSA.egg-info/requires.txt
learnMSA.egg-info/top_level.txt
learnMSA/msa_hmm/Align.py
learnMSA/msa_hmm/AlignInsertions.py
learnMSA/msa_hmm/AlignmentModel.py
learnMSA/msa_hmm/AncProbsLayer.py
learnMSA/msa_hmm/Bidirectional.py
learnMSA/msa_hmm/Configuration.py
learnMSA/msa_hmm/ConvertPriors.py
learnMSA/msa_hmm/DirichletMixture.py
learnMSA/msa_hmm/Emitter.py
learnMSA/msa_hmm/Initializers.py
learnMSA/msa_hmm/MsaHmmCell.py
learnMSA/msa_hmm/MsaHmmLayer.py
learnMSA/msa_hmm/Priors.py
learnMSA/msa_hmm/SequenceDataset.py
learnMSA/msa_hmm/TotalProbabilityCell.py
learnMSA/msa_hmm/Training.py
learnMSA/msa_hmm/Transitioner.py
learnMSA/msa_hmm/Utility.py
learnMSA/msa_hmm/Visualize.py
learnMSA/msa_hmm/Viterbi.py
learnMSA/msa_hmm/__init__.py
learnMSA/msa_hmm/trained_prior/128_True_float32__dirichlet.h5
learnMSA/msa_hmm/trained_prior/128_True_float64__dirichlet.h5
learnMSA/msa_hmm/trained_prior/1_True_float32__dirichlet.h5
learnMSA/msa_hmm/trained_prior/1_True_float64__dirichlet.h5
learnMSA/msa_hmm/trained_prior/256_True_float32__dirichlet.h5
learnMSA/msa_hmm/trained_prior/256_True_float64__dirichlet.h5
learnMSA/msa_hmm/trained_prior/32_True_float32__dirichlet.h5
learnMSA/msa_hmm/trained_prior/32_True_float64__dirichlet.h5
learnMSA/msa_hmm/trained_prior/3_True_float32__dirichlet.h5
learnMSA/msa_hmm/trained_prior/3_True_float64__dirichlet.h5
learnMSA/msa_hmm/trained_prior/64_True_float32__dirichlet.h5
learnMSA/msa_hmm/trained_prior/64_True_float64__dirichlet.h5
learnMSA/msa_hmm/trained_prior/9_True_float32__dirichlet.h5
learnMSA/msa_hmm/trained_prior/9_True_float64__dirichlet.h5
learnMSA/msa_hmm/trained_prior/emissions.log
learnMSA/msa_hmm/trained_prior/transition_priors/delete_prior_1_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/delete_prior_1_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/delete_prior_2_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/delete_prior_2_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_1_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_1_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_2_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_2_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_3_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_3_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_5_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/insert_prior_5_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_10_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_10_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_1_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_1_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_2_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_2_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_3_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_3_float64.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_5_float32.h5
learnMSA/msa_hmm/trained_prior/transition_priors/match_prior_5_float64.h5
learnMSA/protein_language_models/Argparse.py
learnMSA/protein_language_models/BilinearSymmetric.py
learnMSA/protein_language_models/Common.py
learnMSA/protein_language_models/ConvertModels.py
learnMSA/protein_language_models/DataPipeline.py
learnMSA/protein_language_models/ESM2.py
learnMSA/protein_language_models/EmbeddingBatchGenerator.py
learnMSA/protein_language_models/EmbeddingCache.py
learnMSA/protein_language_models/MvnEmitter.py
learnMSA/protein_language_models/MvnMixture.py
learnMSA/protein_language_models/MvnPrior.py
learnMSA/protein_language_models/PretrainMvnPrior.py
learnMSA/protein_language_models/PretrainScoringModel.py
learnMSA/protein_language_models/ProtT5.py
learnMSA/protein_language_models/ProteinBERT.py
learnMSA/protein_language_models/TestPrior.py
learnMSA/protein_language_models/TestScoringModel.py
learnMSA/protein_language_models/TrainingUtil.py
learnMSA/protein_language_models/__init__.py
learnMSA/protein_language_models/pfam_homfam_overlap.txt
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_128_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_128_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_16_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_16_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_32_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_32_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_64_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/esm2_64_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_128_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_128_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_16_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_16_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_32_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_32_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_64_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/protT5_64_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_128_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_128_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_16_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_16_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_32_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_32_softmax.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_64_sigmoid.h5
learnMSA/protein_language_models/new_scoring_models_frozen/proteinBERT_64_softmax.h5
learnMSA/protein_language_models/pretraining/Snakefile
learnMSA/protein_language_models/pretraining/config.yml
learnMSA/protein_language_models/pretraining/results/sigmoid.tbl
learnMSA/protein_language_models/pretraining/results/softmax.tbl
learnMSA/protein_language_models/pretraining/results/test_prior.tbl
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_128_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_16_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_32_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/esm2_64_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_128_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_16_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_32_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/protT5_64_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_128_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_16_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_32_reduced_mix32_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix100_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix100_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix10_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix10_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix1_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix1_softmax.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix32_sigmoid.h5
learnMSA/protein_language_models/priors_V3/proteinBERT_64_reduced_mix32_softmax.h5
learnMSA/protein_language_models/simple/config.yaml
learnMSA/run/__init__.py
learnMSA/run/console.py
logo/logo.pdf
logo/training.gif
logo/training_loop.gif
test/ForwardBenchmark.ipynb
test/ModelA.png
test/ModelB.png
test/RefModels.py
test/TestModels.ipynb
test/TestSupervisedTraining.py
test/TheoreticalFoldedTransitions.ipynb
test/TheoreticalMvnEmittions.ipynb
test/UnitTests.py
test/__init__.py
test/indices
test/keras_metadata.pb
test/meta.json
test/model
test/saved_model.pb
test/data/BB11001.fasta
test/data/KAS.fa
test/data/PF00008_uniprot.fasta
test/data/ambiguous.fasta
test/data/bowman.fasta
test/data/bowman.ref
test/data/egf.fasta
test/data/egf.ref
test/data/empty_seqid.fasta
test/data/empty_sequence.fasta
test/data/faulty_format.fasta
test/data/faulty_msa.fasta
test/data/felix.fa
test/data/felix_insert_delete.fa
test/data/felix_msa.fa
test/data/headers.fasta
test/data/length_diff.fa
test/data/rhv.fasta
test/data/rhv.ref
test/data/simple.fa
test/data/single_sequence.fasta
test/data/test.txt
test/data/unknown_symbol.fasta
test/data/untitled.txt
test/variables/variables.data-00000-of-00001
test/variables/variables.index
util/install_brain.sh
util/run_learnMSA.sh