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  • Global Alignment With Mummer (Parameter for Gap Extension & Opening Cost)

    Dear Sir,

    I am trying to perform global alignment for contigs to several
    chromosomes in genome using Mummer.

    I am wondering what is the parameter I can use for setting the parameter below
    1. Gap Extension Cost (e.g. I want to set it to < 1).
    2. Gap Opening Cost.


    Specifically for "nucmer" script.

    Thanks and hope to hear from you again.

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