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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 input
For the given input file:
```
>sample1
AGACACAGTCAC
>sample1
AGACAC----AC
>sample1
AAACGCATTCAN
```
the output is:
```
>sample1
GAG
>sample1
GA-
>sample1
AGT
```

### 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.