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Recombinant Identification Program: RIP 3.0

Purpose: RIP identifies recombination in a query sequence by calculating its similarity to a background alignment of HIV-1 sequences of different subtypes in a sliding window. For details, see RIP Explanation.

Input Query
Upload your query sequence file
Or paste your query sequence
[Sample Input]
Or enter a GenBank accession number

Input Background
Use HIV database subtype consensus alignment as background
Include CRF01_AE consensus
Select custom background from subtype consensuses
Use your own alignment as background
Upload your alignment here
Or paste your alignment here

Options
Window size
Significance 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
last modified: Wed Apr 15 11:10 2009


Questions or comments? Contact us at seq-info@lanl.gov.