Dataset and R scripts for evo3D manuscript use cases

Use case data sets and code for "evo3D R package: a spatial haplotype framework for structure-informed analysis of molecular evolution".

evo3D links protein structure to multiple sequence alignment (MSA) data, generates spatial windows, and extracts the corresponding MSA subsets for use with downstream genetic statistics. The datasets here cover Hepatitis C virus E1/E2 structure and MSAs as well as analysis scripts to generate figures. With additional datasets and analysis scripts for Chikungunya virus E1/E2, and the test script for computational scaling of table S4. The full package is available at github.com/bbroyle/evo3D.

Contact: Brad Broyles (bbroyle@purdue.edu)

Reference: Bradley K. Broyles, Qixin He. evo3D: a generalised framework for structure-informed evolutionary analysis, implemented in R. bioRxiv 2025.12.12.694041; doi: https://doi.org/10.64898/2025.12.12.694041