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A succinct description of gubbins' method is as follows:

Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity.

Admin notes

The documentation mostly goes over installation via linuxbrew, and looks very convenient. However, linuxbrew is not designed wth clusters in mind, and despite attempts, it causes some problems, so it had to be abandoned.

On the source compilation, there will be problems with libtool versions. You can get over this by

autoreconf --force --install

instead of the "autoreconf -i" as advised int he file.