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 - Hypermut_1052.csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR1052. Table S4 - Hypermut_2038.csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR2038. Table S5 - Hypermut_1114.csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR1114. Table S6 - Hypermut_2028.csv: it contains all the Hypermut results (positives for hypermutations and negatives) of the BR2028. Table S7 - Hypermut_1117.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 extended_lorfs.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 translated_extended_lorfs.fasta. Script.RUN: script used in TNT v1.6 for the phylogenetic tree search under the parsimony optimality criterion. Supplementary Alignments: 1052_aligned.fasta: it contains all sequences from patient BR1052 aligned by Geneious Prime® v2025.0.3. 1114_aligned.fasta: it contains all sequences from patient BR1114 aligned by Geneious Prime® v2025.0.3. 1117_aligned.fasta: it contains all sequences from patient BR1117 aligned by Geneious Prime® v2025.0.3. 2028_aligned.fasta: it contains all sequences from patient BR2028 aligned by Geneious Prime® v2025.0.3. 2038_aligned.fasta: it contains all sequences from patient BR2038 aligned by Geneious Prime® v2025.0.3. 1052_aligned.nexus: it contains all sequences from patient BR1052 aligned by MAFFT v7.0. 1114_aligned.nexus: it contains all sequences from patient BR1114 aligned by MAFFT v7.0. 1117_aligned.nexus: it contains all sequences from patient BR1117 aligned by MAFFT v7.0. 2028_aligned.nexus: it contains all sequences from patient BR2028 aligned by MAFFT v7.0. 2038_aligned.nexus: it contains all sequences from patient BR2038 aligned by MAFFT v7.0. extended_lorfs.fasta: it contains the extended aligned sequences with the longest ORFs from visit two to visit five. Supplementary Other Files: translated_extended_lorfs.fasta: it contains amino acid sequences translated from extended_lorfs.fasta.