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HIV sequence database



Highlighter

Purpose: This tool highlights matches, mismatches, transition and transversion mutations, and silent and non-silent mutations in aligned protein or nucleotide sequences. This tool is particularly useful for visualizing potential recombination and hypermutation in closely-related sequences. See Highlighter Explanation.

  Mismatches   Transitions and Transversions   Silent and Non-silent Mutations   Matches  
Input
Paste your alignment

[Sample Input(na)]
[Sample Input(aa)]
Or upload sequence file
Options
Master(s) Top of the sequences   or  
Sort sequences By similarity Do not sort By tree
        Create NJ tree Upload my tree
Tic width ( <1 makes thinner, >1 thicker)
Sequence type Nucleotides Amino acid
Ignore sequence type check Yes No
Treat gaps as character? Yes No
Handling IUPAC codes Ignore Mark as unknown
Use codes to compare Treat codes as characters   set different colors for each mismatched code
Color scheme Standard Se-Al (default) Se-Al (polar/non-polar) BioEdit

last modified: Fri Nov 3 11:10 2017


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

 
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