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.


Phylogenetic Placement Service

Purpose: To help decide whether a sequence belongs to a known or new clade, this service reports phylogenetic relatedness of a query sequence with reference sequences in known clades. The query sequence is automatically aligned with reference sequences before analysis.


  1. Enter a sequence, in any standard format.
    • Copy and paste your sequence into the text box,
    • Use the "Choose File" button to select a sequence file to upload from your computer.
  2. Choose between analysis methods:
    • Pairwise Distances summarizes the distribution of uncorrected pairwise distances for query and reference sequences. Analysis type allows you to specify the distances to be reported.
    • Branching Index computes a profile of phylogenetic relatedness with known subtypes from overlapping windows over the length of your sequence.
  3. Click on the "Submit" button to start the analysis.

Please consult the documentation for methodological details.

Paste your input here:
[Sample Input]
or upload alignment file
Analysis Method Pairwise Distances Analysis type
Branching Index

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