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HIV sequence database



SUDI Subtyping

(SUbtyping DIstance)

Purpose: This tool helps determine if a newly defined clade of related sequences should be considered a new subtype, a new sub-subtype, or part of a previously defined subtype.

Details: To use this tool, you can either enter a sequence alignment, which is used to create a neighbor joining tree to serve as the basis for the genetic distances, or you can enter your own tree as a PHYLIP outfile. The format of the input sequence names is critical. Please read the SUDI Explanation carefully before using this program.

Input
icon Input type Alignment   PHYLIP outfile
Paste input
[Sample Input]
Or upload file
Options
icon Specify subtypes of sequences  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 labeled with a subtype (example)
        
        
icon What are the subtypes and sub-subtype groupings in your background set?

(The default subtypes listed are a typical set for HIV sequences)
icon Which comparisons should be considered sub-subtype comparisons? x     x     x     x     x
x     x     x     x     x
(The default subtypes listed would be a typical set for HIV sequences).
icon Plot title
last modified: Wed Nov 29 14:32 2017


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

 
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