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APSP_algorithm

This is the implementation of algorithm developed by Loukides and Pissis to solve the all-pairs suffix/prefix (APSP) problem [1]. This algorithm changes the APSP problem to l-APSP, where l defines the minimal overlap of the pairs.

The current implementation does not provide the option to change l.

Running the algorithm

To run the algorithm: ./bin/algorithm INPUT_FILE OUTPUT_FILE

The INPUT_FILE should be a FASTA file and the OUTPUT_FILE will be a tab-delimited file.

References

[1] G. Loukides and S.P. Pissis (2022). All-pairs suffix/prefix in optimal time using Aho-Corasick space. Information Processing Letters, 106275, doi: https://doi.org/10.1016/j.ipl.2022.106275.