SNP-sites

SNP-sites rapidly extracts single nucleotide polymorphisms (SNPs) from multi-FASTA alignment files for downstream population genomic analysis.

Key Features:

• Efficient Resource Usage: SNP-sites processes large alignments using modest RAM and a single CPU core.
• Multiple Output Formats: Results can be output in multiple formats for downstream analysis.
• Cross-Platform Compatibility: The software has been tested on more than 20 operating systems.

Scientific Applications:

• Prokaryotic Population Studies: SNP-sites enables extraction of SNPs from large whole genome alignments for population genomic studies of prokaryotes.

Methodology:

SNP-sites is implemented in C and processes multi-FASTA alignment files to extract SNP positions.