HIV Databases HIV Databases home HIV Databases home
HIV sequence database


Recombinant Identification Program

Purpose: RIP identifies recombination in query sequence(s) by calculating similarity to a background alignment in a sliding window. For details, see RIP Explanation.

Input Query
icon Upload your query sequence(s)
Or paste your query sequence(s)
[Sample Input]
Or enter a GenBank accession
E-mail address   (required if >1 sequence entered)
Input Background
icon Use HIV-1 subtype consensus alignment
icon Customize background from HIV-1 subtypes and CRFs
icon Use your own alignment as background
icon Window size NOTE: window size must be smaller than query!
icon Confidence threshold

icon Gap handling

icon Score multistate characters as partial matches     (applies to nucleotide queries only)


A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences.
Siepel AC, Halpern AL, Macken C, Korber BT.
AIDS Res Hum Retroviruses. 1995 Nov;11(11):1413-6.
Link to: PubMed or text online
last modified: Wed Oct 13 10:44 2021

Questions or comments? Contact us at

Operated by Triad National Security, LLC for the U.S. Department of Energy's National Nuclear Security Administration
© Copyright Triad National Security, LLC. All Rights Reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health