This is the command snp-sites that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
-V
Show version and exit
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
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