Do protein language models understand evolution? Mixed evidence from ancestral sequences and ESM2.

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Data Description

Ancestral Sequence Generation

Ancestral sequences were reconstructed using the workflow in ASR/ASR_notebook.ipynb. All sequence inputs and outputs are in the ASR/ directory.

ESM2 Pseudo-perplexity Calculation

ESM2 pseudo-perplexity scores were calculated using ESM2_scoring/esm2_pppl_calculator.py on a GPU-enable AWS EC2 instance. All inputs and outputs are in the ESM2_scoring/ directory.

Reproduce

Please see SETUP.qmd.

Contribute

Please see CONTRIBUTING.qmd.