HIITE designates the infection stage as either being chronic or incident, and approximates the infection time of those incident subjects. Users can directly upload a single fasta file (number of sequences > 4) onto HITTE for instantaneous processing and output execution. HIITE takes two types of input: i) full envelope gene sequences and ii) envelope gene segment of HXB2 7134-7499 (check “HXB2 7134-7499” option). Check the “Align” command if input sequences need to be aligned [link]. HIITE’s output includes the stage of infection (chronic or incident) along with the Hamming distance distribution plot, diversity, genome similarity index (GSI), and variance. For incident infection cases, estimated days post infection with 95% prediction intervals are provided.
Reference: S. Y. Park, T. M. T. Love, S. Kapoor, and H. Y. Lee, HIITE: HIV-1 Incidence and Infection Time Estimator.Bioinformatics. 2018 Jun 15;34(12):2046-2052. doi: 10.1093/bioinformatics/bty073.