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
 -V		    print version and exit
 <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.

For the given input file:

>sample1
AGACACAGTCAC
>sample1
AGACAC----AC
>sample1
AAACGCATTCAN

the output is:

>sample1
GAG
>sample1
GA-
>sample1
AGT

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

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

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.

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