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What is the default gap penalty using muscle in R?

I'm using the muscle package in R to align multiple sequences, and want to know what gap penalty the algorithm is applying (if any) when the argument "gapopen" is not included 

c <- muscle::muscle(chroma)

The alignment looks fine, but I'd like to know how strictly/leniently gaps are being inserted

Solution

  • The documentation of the muscle package is admittedly poor but at least it refers us to the online documentation of the muscle software. There we find a footnote regarding the default value of the gapopen (and other) parameters:

    Default depends on the profile scoring function. To determine the default, use –verbose –log and check the log file.

    So, to determine the default given your scoring function, rerun the function and pass verbose = TRUE, log = TRUE, and check the log file output.