Hey, I have just updated this tool to the earliest usable version.
It is designed to compare sequence differences (SNPs) inside loci across multiple genomes, and make it easily viewable thru dissimilarity matrixes and clustering.
linkageMapper is written in python and open source.
I don't know if the use cases for this tool are broad, though. I Wrote it to help on my own research.
For example, you choose Lactobacillus plantarum. There is a helper script that automatically downloads a bunch of genomes from NCBI for various strains of this organism so you can just run it and/or place your own genomic fasta files as the readme explains.
Then choose various L. plantarum genomic loci:
pts19D, cinA, and fecB.
The analysis proceeds and you'll know (illustrative) that the strain CECT 9571 is equal to WFCS1 at cinA, but different at fecB, while CECT 9434 is equal to WCFS1 at fecB at cinA.
All the instructions are available at the github page.
EDIT: Forgot to mention that each genomic locus is obtained from the genomes through docking of a start primer and an end primer. This way we can work with multiple genome files while having only one of them annotated. Also, it's possible to compare loci from genomes of different species.