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# 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
-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.
### 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.