README.md

SNP Sites

This program finds snp sites from a multi fasta alignment file.

Usage: snp-sites [-mvph] [-o output_filename] <file>
This program finds snp sites from a multi fasta alignment file.
 -m		    output a multi fasta alignment file (default)
 -v		    output a VCF file
 -p		    output a phylip file
 -o		    specify an output filename
 -h		    this help message
 <file>		input alignment file which can optionally be gzipped

This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in the following formats:

• a multi fasta alignment,
• VCF,
• relaxed phylip format.

Example usage

snp-sites my_alignment.aln
snp-sites my_gzipped_alignment.aln.gz

Multi Fasta Alignment

Similar to the input file but just containing the SNP sites.

VCF

This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation.

Relaxed Phylip format

All the SNP sites in a format for RAxML and other tree building applications.