HIV Databases HIV Databases home HIV Databases home
HIV sequence database



SUDI Subtyping

(SUbtyping DIstance)

Purpose: This tool is designed to help determine if a newly defined clade of related sequences should most appropriately be considered a new subtype, a new sub-subtype, or part of a previously defined subtype.

Details: SUDI should be used in conjunction with other tools that will identify recombination and phylogenetic relationships. The purpose of this tool is to determine tree-based genetic distances for a new cluster relative to known subtypes, and then to compare these distances to typical distances found among pre-existing subtypes.

To use this tool, you can either enter a sequence alignment and create a neighbor joining tree to serve as the basis for the genetic distances, or you can enter your own tree in the form of a PHYLIP outfile. The format of the input sequence names is critical.

Please read the SUDI Explanation carefully before using this program.

Input
Please indicate if input is a sequence alignment or a tree represented as a PHYLIP outfile
Indicate format
Paste input
[Sample Input]
Or upload file
Options
What are the subtypes and sub-subtype groupings in your background set (The default subtypes listed are a typical set for HIV sequences).
     
     
  
Which comparisons should be considered sub-subtype comparisons? (The default subtypes listed would be a typical set for HIV sequences).
      x       x       x       x       x      
      x       x       x       x       x
  
Indicate base node (only required if input is an outfile)
Give the plot a title

NOTE: This program may take some time to finish.
last modified: Thu Apr 29 09:58 2010


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

 
Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © 2005-2012 LANS LLC All rights reserved | Disclaimer/Privacy

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