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HIV Sequence Database



RAPR

Recombination Analysis PRogram

Purpose: See RAPR Explanation.

Input
Paste your alignment

[Sample Input]
Or upload sequence file
Options
FDR cut
TF/Lineages

Assign lineages according to TFs or CONSENSUS
   top sequence(s) in the alignment
Automatically, according to sequence names
   the column in field of names delimited by
   first character(s) in names
Manually
   paste or upload grouped sequence names labelled with a lineage (example)
        
        

Time points No time points available
Run ancestral recombination only
Specify time points
Automatically, according to sequence names
   the column in field of names delimited by
   first character(s) in names
Manually
   paste or upload grouped sequence names labelled with a time point (example)
        
        

Deletions Should deletions be included in RAPR statistics?
No
Yes, include deletions at the following positions
      
ElimDupes Are all sequences in the input unique?
No, I need to run ElimDupes or I'm not sure.
Yes, all sequences are unique and sequence names are in ElimDupes format
Email results

Reference:

last modified: Thu Dec 9 18:03 2021


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

 
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