The default parameters appear to work reasonably well over a range of
divergences although at higher levels of nucleotide divergence, e.g.
<65% identity, the aligner begins to lose sensitivity. When this happens
some positionally homologous sites fail to become aligned. This issue is
characterized
Dear Aaron,
I did not imply a bug, maybe there is something with the settings I used to
create the SuperGenome. I was just wondering if the default settings for the
progressiveMauve algorithm were acceptable if I have varying degrees of
similarity between the genomes?
Kind regards,
Anja
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