.gitignore
LICENSE
Makefile
README.md
pyproject.toml
.github/workflows/build-and-test.yml
.github/workflows/pypi-publish.yml
data/wyatt-10x-1p5m_paired-merged_fs-all_pcp_2024-11-21_no-naive_sample100_DXSM_Valid.csv.gz
data/wyatt-10x-1p5m_pcp_2023-11-30_NI.first100.csv.gz
examples/bidirectional_transformer.yaml
examples/parent_independent.yaml
examples/single.yaml
examples/transformer_large.yaml
examples/transformer_sml.yaml
netam/__init__.py
netam/attention_map.py
netam/cli.py
netam/codon_table.py
netam/common.py
netam/dasm.py
netam/data_format.py
netam/ddsm.py
netam/dnsm.py
netam/dxsm.py
netam/framework.py
netam/hit_class.py
netam/hyper_burrito.py
netam/model_factory.py
netam/models.py
netam/molevol.py
netam/multihit.py
netam/oe_plot.py
netam/pretrained.py
netam/sequences.py
netam/whichmut_dataset.py
netam/whichmut_trainer.py
netam.egg-info/PKG-INFO
netam.egg-info/SOURCES.txt
netam.egg-info/dependency_links.txt
netam.egg-info/entry_points.txt
netam.egg-info/requires.txt
netam.egg-info/top_level.txt
netam/model_configs/bidirectional_default.yaml
netam/model_configs/parent_independent_default.yaml
netam/model_configs/single_default.yaml
netam/model_configs/transformer_large.yaml
netam/model_configs/transformer_small.yaml
notebooks/README.md
notebooks/dasm_demo.ipynb
notebooks/dnsm_demo.ipynb
notebooks/thrifty_demo.ipynb
tests/conftest.py
tests/test_ambiguous.py
tests/test_backward_compat.py
tests/test_codon_table.py
tests/test_dasm.py
tests/test_ddsm.py
tests/test_dnsm.py
tests/test_framework.py
tests/test_model_factory.py
tests/test_molevol.py
tests/test_multihit.py
tests/test_netam.py
tests/test_parent_independent_mask.py
tests/test_pretrained.py
tests/test_sequences.py
tests/test_simulation.py
tests/test_tokens.py
tests/test_whichmut_trainer.py
tests/old_models/ddsm_13k-v1jaffe+v1tang-joint.pth
tests/old_models/ddsm_13k-v1jaffe+v1tang-joint.yml
tests/old_models/ddsm_output
tests/old_models/dnsm_13k-v1jaffe+v1tang-joint.pth
tests/old_models/dnsm_13k-v1jaffe+v1tang-joint.yml
tests/old_models/dnsm_output
tests/old_models/val_branch_lengths.csv
tests/old_models/val_predictions.pt