LICENSE
README.md
pyproject.toml
setup.py
evo/__init__.py
evo/littrain.py
evo/data_format/DataFormat.py
evo/data_format/run_tokenizer/__init__.py
evo/data_format/run_tokenizer/open_tokenizer.py
evo/data_format/run_tokenizer/tokenizer_trainer.py
evo/loss/EvoLoss.py
evo/loss/__init__.py
evo/model/EvoMamba.py
evo/model/LitEvo.py
evo/model/__init__.py
evo/model/utils_evo/EvoMamba_old.py
evo/model/utils_evo/FinalRegressor.py
evo/model/utils_evo/VideoMamba.py
evo/model/utils_evo/download_weights.py
evo/model/utils_evo/evo-download.py
evo/model/utils_evo/learning.py
evo/model/utils_evo/load_evo.py
evo/model/utils_evo/test_videoMamba.py
evo/model/utils_evo/tools.py
evo/model/utils_evo/testing_functions/evo_download.py
evo/model/utils_evo/testing_functions/gpu_check.py
evo/model/utils_evo/testing_functions/inference.py
evo/model/utils_evo/testing_functions/test_data.py
evo/model/utils_evo/testing_functions/test_evo.py
evo/model/utils_evo/testing_functions/test_generate.py
evo/model/utils_evo/testing_functions/test_load_evo.py
evo/model/utils_evo/testing_functions/generate/reference_evo_generate.py
plasmidai/__init__.py
plasmidai/paths.py
plasmidai/utils.py
plasmidai.egg-info/PKG-INFO
plasmidai.egg-info/SOURCES.txt
plasmidai.egg-info/dependency_links.txt
plasmidai.egg-info/top_level.txt
plasmidai/data/__init__.py
plasmidai/data/scripts/1_filter.py
plasmidai/data/scripts/2_partition.py
plasmidai/data/scripts/__init__.py
plasmidai/data/tokenizers/1_tokenizer_bpe.py
plasmidai/data/tokenizers/2_tokenizer_nt.py
plasmidai/data/tokenizers/__init__.py
plasmidai/datasets/__init__.py
plasmidai/datasets/plasmid.py
plasmidai/datasets/replicons.py
plasmidai/datasets/utils.py
plasmidai/experimental/__init__.py
plasmidai/experimental/callbacks.py
plasmidai/experimental/lit.py
plasmidai/experimental/optimizers.py
plasmidai/experimental/sample.py
plasmidai/experimental/train.py
valid/__init__.py
valid/batch-wide_analysis/__init__.py
valid/batch-wide_analysis/check_dependency_conflicts.py
valid/batch-wide_analysis/mobsuite_analysis.py
valid/batch-wide_analysis/tools.py
valid/batch-wide_analysis/generated_sequences/convert_to_fasta.py
valid/plasmid_classification/__init__.py
valid/plasmid_classification/sequential_alignment_v2.py