gaal (Gappy Aligner) is a free and open-source Java library that implements an Enhanced Suffix Array and a Linearized Suffix Tree.
gaal was developed with a flexible API in mind and allows for any type of underlying sequences, sorting algorithms etc. to be used.
Moreover, gaal provides an implementation of a so-called Embedded Suffix Tree, which could be used to discover discontinuous (gappy) repeats.
Finally, a basic vector-space-model-based aligner is included for repeat alignment.
Requirements:
· Java
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