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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
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 is entered
Input Background
Use HIV-1 subtype consensus alignment as background   includes subtypes A - K
Include CRF01_AE consensus
Select custom background from HIV-1 subtype sequences
Use your own alignment as background NOTE: this set cannot contain more than 26 sequences!
Align your query and custom background Check box if custom background is not aligned with query.
Upload background alignment
Or paste background alignment
Window size NOTE: window size must be smaller than query!
Confidence threshold

Gap handling Treat gaps as characters; Plot all window values.
Treat gaps as characters; Don't plot window values for gaps.
Strip all gaps; Plot all window values.
Strip all gaps; Plot blanks where gaps used to be.
Multistate characters match partially True    False


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.
PMID: 8573400

last modified: Tue Dec 3 11:33 2013

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