Question: Implementation of Alignment with convex gap penalty
0
gravatar for Fadel
2.8 years ago by
Fadel10
Malaysia
Fadel10 wrote:

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

alignment • 704 views
ADD COMMENTlink written 2.8 years ago by Fadel10
2

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 2.8 years ago by Brian Bushnell16k

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

ADD REPLYlink written 2.8 years ago by Fadel10
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