I was wondering what the difference between the original Mauve algorithm and progressiveMauve is.
The official website states that the difference will be explained in "a later section" but I can't find it. When I want to align my genomes with original Mauve in the GUI version, it informs me that progressiveMauve has superseded the original one.
I get that progressiveMauve is an updated version of the old one. But what exactly is the difference?