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:

       a multi fasta alignment, VCF, relaxed phylip format.

OPTIONS

       -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 document

EXAMPLES

       snp-sites my-alignment.aln

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

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)

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.

                                            03/28/2014                            SNP-SITESDOC(1)