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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
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
First sequence compared to others
Corrected statistics

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: Tue Mar 10 09:43 2020

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