Hi, do you know what does parallel lines from nucmer plot means?
These are a type of “alignment” graph. Specifically, where the tool found the best fit between the sequences when compared. Bases 0-750k have one “aligned region” then 750k-4500k have another.
And, I think the slope directions indicate sequence orientation but not 100% sure … so double check my work on that and feel free to post back any factual information you find about that!!
An internet search will find much more discussion, including the author help. Or, you can try the links at the bottom of the tool form. Any scientific advice for the tool itself would apply when using it through Galaxy.