---
name: "snp-sites"
section: "1"
platform: "linux"
package: "snp-sites"
version: "2.5.1-2+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/snp-sites"
---

# snp-sites(1)

finds SNP sites from a multi FASTA alignment file

## NAME

snp-sites - finds SNP sites from a multi FASTA alignment file

## SYNOPSIS

snp-sites \[-mvph\] \[-o output\_filename\] \[input file\]

## DESCRIPTION

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

• multi fasta alignment

• VCF

• relaxed phylip format

## OPTIONS

- **-r**

  Output internal pseudo reference sequence

- **-m**

  Output a multi fasta alignment file (default)

- **-v**

  Output a VCF file

- **-p**

  Output a phylip file

- **-c**

  Only output columns containing exclusively ACGT

- **-b**

  Output monomorphic sites, useful for BEAST

- **-o**

  Specify an output filename

- **-h**

  Show help message

- **-V**

  Show version and exit

## EXAMPLES

```
snp-sites my-alignment.aln
```

```
snp-sites my-gzipped-alignment.aln.gz
```

```
snp-sites -cb -o output_beast_format.aln inputfile.aln
```

## FORMAT OF THE INPUT FILE

Input files should look like this:

```
>reference_sequence
aaccggtt
>comparison_sequence
AACCGGTT
>another_comparison_sequence
AACCGCTT
```

For more examples, visit:  \<https://github.com/sanger-pathogens/snp-sites/tree/master/tests/data\>

## AUTHOR

snp-sites was originally written by Andrew Page ( \<ap13@sanger.ac.uk\>)

## CITATION

If you use this program, please cite: "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris (2016), bioRxiv doi:  \<http://dx.doi.org/10.1101/038190\>

## COPYING

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.