Implementation of Alignment with convex gap penalty

Question

[Fadel]

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

[Brian Bushnell]

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.

[Fadel]

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