Question: Implementation of Alignment with convex gap penalty
gravatar for Fadel
3.7 years ago by
Fadel20 wrote:

Im looking for implementation of alignment with convex gap penalty model in any programming language ?

alignment • 846 views
ADD COMMENTlink written 3.7 years ago by Fadel20

BBMap uses a multi-affine gap penalty, which is similar to a logarithmic gap penalty. It's open-source. Probably, a logarithmic (or similar) gap penalty would be slightly better, since the current implementation uses fixed steps rather than a continuous penalty.

ADD REPLYlink written 3.6 years ago by Brian Bushnell17k

thanks a lot Brian :)) I will have look at BBMap

ADD REPLYlink written 3.6 years ago by Fadel20
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