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".
The supplementary materials contain the supplementary datasets and figure-analysis scripts. Details on file organization, available datasets, execution limitations, and the complete file inventory with MD5 checksums are provided in the information for reviewers (Markdown | PDF).