HIV Databases HIV Databases home HIV Databases home
HIV sequence database

SNAP v2.1.1

Synonymous Non-synonymous Analysis Program

Purpose: SNAP calculates synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences.

Details: Please read the Readme file before using this program! For alignments smaller than 40 sequences the results will be displayed on our web site. For larger alignments (more than 40 sequences) you will receive a job title and reference number and results will be emailed to you. Alternatively, you can download the Perl version of SNAP and process your data on your local machine.
Input sequences must be codon-aligned nucleotides. The tool automatically recognizes several common sequence formats. If your input format is not accepted, web-based format conversion sites are available.

WARNING: Unaligned sequences or aligned sequences copied from Word (containing non-ASCII characters) may cause the program to crash or give meaningless output.

References: If you use SNAP in a paper, please reference both the HIV database website ( and the following paper. You may also need to reference other papers cited in the Readme file.

  • Korber B. (2000). HIV Signature and Sequence Variation Analysis. Computational Analysis of HIV Molecular Sequences, Chapter 4, pages 55-72. Allen G. Rodrigo and Gerald H. Learn, eds. Dordrecht, Netherlands: Kluwer Academic Publishers.
Paste codon alignment
or upload alignment file

In addition to summary table, show XYPLOT of the cumulative behavior of the average synonymous and non-synonymous substitutions as you move across the coding region.
NJ tree based on synonymous distances
NJ tree based on nonsynonymous distances
SNAP statistics

Job info
Enter a job title
Enter your email for job results to be sent

Release Notes: For details on releases click here.

Known Bugs: For known bugs click here.

Wish List: For desired new features click here.

last modified: Fri Apr 3 12:17 2015

Questions or comments? Contact us at

Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © 2005-2012 LANS LLC All rights reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health