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.


Purpose: PCOORD (Principal Coordinate Analysis) is a procedure to find meaningful patterns in sequence data.

Details: The Principal Coordinate Analysis method was developed by the mathematician J.C. Gower in 1966. This web interface uses the PCOORD program suite, written by Des Higgins. The procedure takes an alignment as input, and summarizes the variation in the sequences in 10 'axes' or 'dimensions'. Each sequence gets a score on each of the dimensions, and these scores can be plotted pairwise. For additional details, see PCOORD Explanation.

This tool attempts to automatically recognize the format of your input file. If this fails, you can use our Format Converter to convert your alignment to Fasta, and use that for input. This program can currently handle a maximum of 1000 sequences of 12,000 length; for inputs of more that 500 sequences, the program will be executed in the background, and you will receive an email when the results are available.

Paste your input here
[Sample Input]
or upload your file

Strip alignment gaps? yes no
Select distance matrix type ID distances Smith AA matrix

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