This repository contains core data files for the Primate Genome-phenome Archive (PGA), a curated resource integrating genetic and phenotypic information from non-human primates.
The PGA dataset is part of the project Valenzuela et al., 2025, and provides a foundation for evolutionary, biomedical, and comparative analyses linking genotype to phenotype across primates.
├── genetic.information
│ ├── ALL_RER_CONVERGE_UNIQUE_MAR23.txt
│ └── CAAS_FINAL_MAR23.tab
├── LICENSE
├── phenotype.tables
│ ├── caas.discovery.groups.csv
│ ├── caas.results.csv
│ ├── human.equivalent.measurements.csv
│ ├── metadata.qualitative.traits.csv
│ ├── metadata.quantitative.traits.csv
│ ├── nhp.phenomic.dataset.csv
│ ├── trait.data.sources.csv
│ └── traits.redundancy.csv
└── README.md
This folder contains gene-level evolutionary signals, including:
- CAAS_FINAL_MAR23.tab: Final list of convergent amino acid substitutions (CAAS) detected across primates.
- ALL_RER_CONVERGE_UNIQUE_MAR23.txt: Genes showing significant rate shifts (RERconverge) associated with phenotype convergence.
This folder includes phenotype tables describing ~230 traits measured across ~220 primate species. The data include:
- Trait metadata (quantitative and qualitative)
- Cross-species harmonization (e.g., human equivalent units)
- Trait grouping and redundancy curation
- Results of gene-trait association analyses
For a detailed explanation of each file, please refer to the official PGA documentation:
📄 Download the PDF documentation
This repository is distributed under the GNU General Public License v3.0.
See the LICENSE file for details.
Part of the project "Valenzuela et al., 2025".