.gitignore
.readthedocs.yaml
LICENSE
README.md
environment-epi.yml
requirements.txt
setup.py
bin/benchmark.py
bin/benchmark.sh
bin/benchmark_downsample.py
bin/benchmark_downsample.sh
bin/benchmark_esm1v.py
bin/benchmark_esm1v.sh
bin/clustal2newick.py
bin/cov.py
bin/cyc.py
bin/dms.py
bin/eno.py
bin/evolocity_graph.py
bin/fasta2nexus.py
bin/fasta2phylip.py
bin/fb_model.py
bin/fb_semantics.py
bin/flu.py
bin/flu_np.py
bin/gag.py
bin/glo.py
bin/hiv.py
bin/language_model.py
bin/locations.py
bin/main.sh
bin/mammals.py
bin/mutation.py
bin/newick_reformat.py
bin/pgk.py
bin/phylo_eno.sh
bin/phylo_np.sh
bin/phylo_pgk.sh
bin/phylo_ser.sh
bin/plot_dms.py
bin/plot_dms_selection.py
bin/plot_epitopes.py
bin/plot_np_edges.py
bin/pseudotime_reproducibility.py
bin/ser.py
bin/tape_model.py
bin/tape_semantics.py
bin/transformer_layers.py
bin/uniref_taxonomies.py
bin/utils.py
bin/xml_to_fasta.py
docs/Makefile
docs/README.rst
docs/cyc_stream.PNG
docs/index.rst
docs/make.bat
docs/requirements.txt
docs/source/api.rst
docs/source/conf.py
docs/source/index.rst
docs/source/installation.rst
docs/source/references.rst
docs/source/_ext/edit_on_github.py
docs/source/_templates/autosummary/base.rst
docs/source/_templates/autosummary/class.rst
evolocity/__init__.py
evolocity/datasets.py
evolocity/logging.py
evolocity/pl.py
evolocity/pp.py
evolocity/settings.py
evolocity/tl.py
evolocity.egg-info/PKG-INFO
evolocity.egg-info/SOURCES.txt
evolocity.egg-info/dependency_links.txt
evolocity.egg-info/requires.txt
evolocity.egg-info/top_level.txt
evolocity/plotting/__init__.py
evolocity/plotting/docs.py
evolocity/plotting/evolocity_plotting.py
evolocity/plotting/palettes.py
evolocity/plotting/scatter.py
evolocity/plotting/utils.py
evolocity/plotting/velocity_contour.py
evolocity/plotting/velocity_embedding.py
evolocity/plotting/velocity_embedding_grid.py
evolocity/plotting/velocity_embedding_stream.py
evolocity/preprocessing/__init__.py
evolocity/preprocessing/featurize_seqs.py
evolocity/preprocessing/neighbors.py
evolocity/preprocessing/utils.py
evolocity/tools/__init__.py
evolocity/tools/fb_model.py
evolocity/tools/fb_semantics.py
evolocity/tools/random_walk.py
evolocity/tools/tape_model.py
evolocity/tools/tape_semantics.py
evolocity/tools/terminal_states.py
evolocity/tools/transition_matrix.py
evolocity/tools/utils.py
evolocity/tools/velocity_embedding.py
evolocity/tools/velocity_graph.py
evolocity/tools/velocity_model.py
evolocity/tools/velocity_onehot.py
evolocity/tools/velocity_pseudotime.py
results/benchmark_downsample_results.txt
results/benchmark_esm1v_results.txt
results/benchmark_results.txt
results/dms_results.csv
tests/test_basic.py