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 When I want to align my genomes with original Mauve in the GUI version, it informs me that progressiveMauve has superseded the original one.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?
See also this link:
There are many interesting points there, including these two below:
"The progressiveMauve algorithm: addressing limitations of the original algorithm
Comparative genomics has revealed that closely-related bacteria often have highly divergent gene content. While the original Mauve algorithm could align regions conserved among all organisms, the portion of the genome conserved among all taxa (the core genome) shrinks as more taxa are added to the analysis. As such, the original Mauve algorithm did not scale well to large numbers of taxa because it could not align regions conserved among subsets of the genomes under study. progressiveMauve employs a different algorithmic approach to scoring alignments that allows alignment of segments conserved among subsets of taxa. The progressiveMauve algorithm has been described in Aaron Darling's Ph.D. Thesis, and is also the subject of a manuscript published in PLoS ONE. A brief overview is given here."
" Strengths of the progressiveMauve algorithm