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allpairs_global All-vs-all global alignment
allpairs_local All-vs-all local alignment
pairs_global Make pair-wise global alignments
pairs_local Make pair-wise local alignments
sam_filter Convert SAM alignments to BLAST6 or human-readable format
search_16s Find 16S genes in chromosomes or contigs
search_pcr Search for amplicons (matches to primer pairs)
sortbylength Sort by decresing sequence length
sortbysize Sort by decresing abundance (size= annotations)
udb2bitvec Create bit vector index for search_16s