Purpose: RIP helps identify recombination in a query sequence by calculating its similarity to a background alignment of HIV-1 sequences of different subtypes in a sliding window.
Usage: Each RIP job requires two inputs from the user, a query sequence, and a background alignment. The total number of sequences is limited to 50. There are 3 options for providing the background alignment.
Window size and significance threshold are adjustable. Alignment gaps may be treated in four different ways. Multistate character codes (IUPAC) in your alignment can be scored as partial matches or as mismatches. When your analysis is complete you can create an illustration of the recombinant genome with our Recombinant HIV-1 Drawing Tool.
For additional details, see RIP Explanation.