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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! You can also download the Perl version of SNAP and process your data on your local machine.

Paste alignment
[Sample Input]
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
Count stop codons

Job info
Job title
E-mail for results to be sent

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.

An excellent suite of tools for studying natural selection can be found on Datamonkey (

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: Thu Jan 21 15:07 2016

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