# Pairwise SNP differences

This is an R script to obtain summaries of pairwise SNP differences for any 
grouping of samples (e.g., MLST groups, monophyletic clades, etc).

# Downloading the script

Clone the git-hub repository. Information on the bar to the right of this window.

# How it works

The script can be run from the command line:

    Rscript<.exe> summarise_snp_differences.R --help
  
Or, from within `R`. Details of variables that should be changed can be found
in the script header.

# Tutorial

A brief tutorial describing the background can be found in the file:

    pairwise_snp_differences.pdf
    
# RStudio

The whole repo can be cloned, and opened as an `RStudio` project. Within `RStudio`
the `.Rmd` file can be easily made into an `.html` file for viewing in a web-browser.