See also this link:

https://testtoolshed.g2.bx.psu.edu/repository/display_tool?repository_id=b44f986fface6d38&tool_config=%2Fsrv%2Ftoolshed%2Ftest%2Fvar%2Fdata%2Frepos%2F001%2Frepo_1703%2Fprogressivemauve.xml&changeset_revision=0622cb9ae2e9

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

It can be applied to a much larger number of genomes than the original Mauve algorithm
It can align more divergent genomes than the original algorithm. 
Genomes with as little as 50% nucleotide identity can be alignable
Manual adjustment of the alignment scoring parameters is usually not necessary
It aligns the pan-genome, e.g. regions conserved among subsets of the input genomes
It is more accurate than the previous Mauve algorithm

"