This is the Linux app named JAligner whose latest release can be downloaded as NAligner-Core-v0.2.zip. It can be run online in the free hosting provider OnWorks for workstations.
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DESCRIPTIONJAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.
This is an application that can also be fetched from https://sourceforge.net/projects/jaligner/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.