HIV-1 Multiple Infections, Recombination, and Hypermutation During a 12-Month Prospective Study of Five HIV-1 Infected Individuals

Supplementary tables: Table S1 - jpHMM. csv: it contains all the recombination results (positives and negatives) generated by jpHMM for all patients. Table S2 - SimPlot. csv: it contains all the recombination results (positives and negatives) generated by SimPlot++ for all patients. Table S3 - Hypermut₁052. csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR1052. Table S4 - Hypermut₂038. csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR2038. Table S5 - Hypermut₁114. csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR1114. Table S6 - Hypermut₂028. csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR2028. Table S7 - Hypermut₁117. csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR1117. Supplementary scripts: LORFS. py: a Python script that extends sequences containing the longest ORFs of the patient sequences from visit two to visit five. The script adjusts the fragments to be multiples of three (codons) in the first reading frame. These sequences may include stop codons but are guaranteed to contain the longest ORF. It generates a file named extendedₗorfs. fasta. Translate. py: a Python script that translates the nucleotide sequences in frame 1 from the patients included in this study. It generates a file named translatedₑxtendedₗorfs. fasta. Script. RUN: script used in TNT v1. 6 for the phylogenetic tree search under the parsimony optimality criterion. Supplementary Alignments: 1052ₐligned. fasta: it contains all sequences from patient BR1052 aligned by Geneious Prime® v2025. 0. 3. 1114ₐligned. fasta: it contains all sequences from patient BR1114 aligned by Geneious Prime® v2025. 0. 3. 1117ₐligned. fasta: it contains all sequences from patient BR1117 aligned by Geneious Prime® v2025. 0. 3. 2028ₐligned. fasta: it contains all sequences from patient BR2028 aligned by Geneious Prime® v2025. 0. 3. 2038ₐligned. fasta: it contains all sequences from patient BR2038 aligned by Geneious Prime® v2025. 0. 3. 1052ₐligned. nexus: it contains all sequences from patient BR1052 aligned by MAFFT v7. 0. 1114ₐligned. nexus: it contains all sequences from patient BR1114 aligned by MAFFT v7. 0. 1117ₐligned. nexus: it contains all sequences from patient BR1117 aligned by MAFFT v7. 0. 2028ₐligned. nexus: it contains all sequences from patient BR2028 aligned by MAFFT v7. 0. 2038ₐligned. nexus: it contains all sequences from patient BR2038 aligned by MAFFT v7. 0. extendedₗorfs. fasta: it contains the extended aligned sequences with the longest ORFs from visit two to visit five. Supplementary Other Files: translatedₑxtendedₗorfs. fasta: it contains amino acid sequences translated from extendedₗorfs. fasta.