I'm having trouble understanding what Mauve's LCB parameter really is. The manual defines it as " the minimum number of matching nucleotides identified in a collinear region for that region to be considered true homology versus random similarity. " I don't even understand what the seed weight really is.
What if I wanted to allow only .02 alignment error, how can I do that? I just don't see how it can be reliable to align with the default LCB then play with the slider until no more "spurious" rearrangements appear.
I would appreciate your clarification. Thank you.