AUTO-TUNE Data Repository

This repository contains datasets utilized in the AUTO-TUNE manuscript for inferring HIV transmission clusters based on genetic distances.

Repository Structure

• lanl/: Data extracted from the Los Alamos National Laboratory database.
• lanl-fl/: Full-length sequences from LANL database, used for comprehensive analyses.
• hiv-pol/: HIV-1 pol gene sequences used in various analyses within the study.
• hcv/: Hepatitis C virus sequences used for comparative analyses.
• clustunr/: Data related to the clustuneR comparison study.

Each directory contains sequence data and results files from analyses conducted using AUTO-TUNE.

Citation

Weaver, Steven, et al. "AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS." bioRxiv (2024).