HCV Database
HCV sequence database
 



To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.


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(aa)]
[Sample Input(na)]
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 Amino acid Nucleotides
Ignore sequence type check Yes No
Treat gaps as character? Yes No
Handling IUPAC codes Ignore Use codes to compare Treat codes as characters Mark as unknown
Color scheme Standard Se-Al (default) Se-Al (polar/non-polar) BioEdit




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