Using Mummer And Deciding Which Alignment Program To Run

Question

[Love]

I need pairwise alignment for the specific two human sequences(10kb each) so that I can compare their similarity. There are five most commonly used programs in the MUMmer package: mummer, nucmer, promer, run-mummer1 and run-mummer3.

So which one is best? Thanks,

Answer 1

[Vitis]

I usually just go with the nucmer command and tune the parameters with multiple runs. promer is for protein alignment, and run-mummer1 and run-mummer3, I believe, are wrapper scripts to run nucmer/promer. Correct me if I'm wrong, as I have not been using it for a while.