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HIV sequence database



Align Multi-tool

Purpose: Simple manipulations of sequence alignments, including sorting, pruning, renaming, and slicing. See explanation.

  Sort   Prune   Rename   Slice & Concatenate  
Input
Paste your alignment

[Sample Input]
Or upload alignment file
Options
Sort by  

icon
  (works when part of names contains subtype)
     Subtype is in field of names delimited by
     (See explanation for ordering and naming conventions.)
in
Delimit names with   
sort by field of names in [add more levels to sort]

icon
 
Tree tool
Model
Site rates
  
Model
# of categories    
Join option      
Outgroup

      
      

icon
  Hamming distance from the top sequence in
Gaps      

icon
 
       
       
    
    

icon
 
 
Pick top sequence
icon
 


Options
Export names  
Save sequence names to text file
Check uniqueness  
Find duplicate names
Replace names with  
icon
 
Accession must be in input seq name to search database

is in field of names delimited by
Numbering fields composing a new name
Subtype Country Year Name
Accession Patient code SE ID Patient ID
Field separator Missing character for unavailable values
icon
  Starting number     Prefix     Suffix
 
icon
 
 
Options
Prune sequnces by  

icon
  (for pattern, simple regex allowed)
Match type
 
Match against
of names delimited by

icon
 
 
Invert
icon
 
 
Squeeze gaps
icon
 
Upload alignment file(s) icon

[Sample Input]

  •          Range
             Range numbers refer to icon

    Click & drag arrows to change order of alignments
 

last modified: Tue Mar 17 20:35 2020


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

 
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