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.

Complete polyprotein

This page provides access to a series of graphs showing the genotype and subtype variability of all HCV proteins. The alignments used for these graphs are the gene alignments that are provided on this website. These alignments are "clean", meaning they have been stripped of related or very similar sequences. Three variability measures are provided: a histogram of the frequency of pairwise distances within genotypes and subtypes; a sliding window graph of the entropy of each protein, and a position-by-position plot of the estimates of ds (synonymous changes) and dn (non-synonymous changes) of each protein. Only genotypes/subtypes represented by a minimum of five sequences are included in these graphs. The tree below is a Neighbor-joining tree (F84 distances, 9194 nt) of the complete genome sequences that formed the basis for the plot of the complete genome distances. Please note that the tree is based on nucleotide rather than amino acid distances, and genotypes with fewer than 5 representatives were also included in the tree.

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