This is an R script to obtain summaries of pairwise SNP differences for any grouping of samples (e.g., MLST groups, monophyletic clades, etc).
Clone the git-hub repository. Information on the bar to the right of this window.
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.
A brief tutorial describing the background can be found in the file:
pairwise_snp_differences.pdf
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.