A software application for rapidly extracting SNPs from a multi-FASTA alignment.

Download and Installation

Please see our GitHub page for download and installation instructions.

Learn and Support

For more information and advice on using this software please see our GitHub page.

License and Citation

SNP-sites is available under GPL3.

If you make use of this software in your research, please cite as:

"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)


If you need help or have any queries, please contact us using the details below.

Our normal office hours are 8:30-17:00 (GMT) Monday to Friday.


Sanger Contributors


  • SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.

    Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al.

    Microbial genomics 2016;2;4;e000056

Tool Type