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snp-sites website  

We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.

Required Modules


  • snp-sites

System Variables

  • HPC_SNP-SITES_DIR - installation directory


If you publish research that uses snp-sites you have to cite it as follows:

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