Example founder conserved sites

Conserved sites (indexed at 1) for the gp120 DEMB11US006 sequence, which is used as an example founder sequence throughout the package. These sites were identified using the identify_conserved_sites() function with the full HIV ENV filtered alignment from the LANL HIV database. See hiv_env_flt_2022 for more details and the link to the entire alignment.

Usage

founder_conserved_sites

Format

founder_conserved_sites

Vector of conserved nucleotides for the gp120 gene of DEMB11US006 (founder), named by the sequence position (indexed at 0)

Source

Full alignment used: https://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html Founder sequence: https://www.sciencedirect.com/science/article/pii/S0022175914000143?via%3Dihub https://www.hiv.lanl.gov/components/sequence/HIV/asearch/query_one.comp?se_id=KC473833