Supporting Information for Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations - Code

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Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations

This is the code repository for the paper (https://doi.org/10.1007/978-3-030-58112-1_27).

We use data from NCBI RefSeq (see prokaryotes.csv) in amino acid format. From the NCBI genome list, FTP URLs are shown to download the files. The amino acid format files end in "_protein.faa.gz".

Data is available at https://doi.org/10.20391/e74e16cc-aa91-41b2-99d7-04465c23cf0a. The list of genomes we used for the testing of the minimisation of the number of Lyndon factors and balancing the length of Lyndon factors is in testingGenomeList. The name of the genome we used for finding the mutation operator to use for the EA is in trainingGenome.

In our code, ModifiedDuvals was the working name of Flexi-Duval. Similarly, ModifiedDuvalsOperator refers to the LF-inspired operator.

NCBI have reduced the number of reference genomes https://ncbiinsights.ncbi.nlm.nih.gov/2020/02/14/assembly-changes/.
Date made available05 Sept 2020
PublisherPrifysgol Aberystwyth | Aberystwyth University
Date of data production27 May 2020
  • Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations

    Major, L., Clare, A., Daykin, J., Mora, B., Peña Gamboa, L. & Zarges, C., 31 Aug 2020, Parallel Problem Solving from Nature – PPSN XVI - 16th International Conference, PPSN 2020, Proceedings: 16th International Conference, Leiden, The Netherlands, September 5-9, 2020, Proceedings. Bäck, T., Preuss, M., Deutz, A., Emmerich, M., Wang, H., Doerr, C. & Trautmann, H. (eds.). Springer Nature, p. 390-403 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12269 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)

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