Decoding the Genotype-Phenotype
Map of Vision

An open-source ecosystem curating visual physiology data and pioneering machine learning approaches to predict opsin phenotypes directly from amino-acid sequences.

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Our Primary Repositories

Open-source datasets and computational tools developed by the Visual Physiology DB organization.

VPOD v1.3

The Visual Physiology Opsin Database is a newly compiled database containing 1,714 unique opsin genotypes and corresponding λmax phenotypes collected across all animals from 120+ publications.

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OPTICS v1.3

The Opsin Phenotype Tool for Inference of Color Sensitivity uses machine learning models trained on VPOD to predict λmax from unaligned sequences and map feature importance to 3D structures.

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Recent Publications

Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype Map

Seth A. Frazer, Todd H. Oakley. bioRxiv, 2025.08.22.671864.

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Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

Seth A. Frazer, Mahdi Baghbanzadeh, Ali Rahnavard, Keith A. Crandall, & Todd H Oakley. GigaScience, 2024.09.01.

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