bioinformatics clustering smith-waterman needleman-wunsch fasta transcription sequence-alignment pairwise-alignment gc-content multiple-sequence-alignment clustalw hirschberg biosequences phylogenetic-dendrograms hierarchical-cluster-analysis

optimization generative-model model-based-optimization blackbox-optimization biosequences offline-setting

genome alphabet evolutionary-algorithms permutations factorization evolutionary-algorithm evolutionary-computation bioinformatics-algorithms factorisation factorization-algorithm lyndon lyndon-factors alphabet-reordering alphabet-ordering biosequences duval duval-s lyndon-words string-factorization string-factorisation