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GAME:
genetic algorithm based motif elicitation
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PLAST-ncRNA: Partition function Local
Alignment Search Tool for non-coding RNA sequences
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Searching for evolutionary distant RNA
homologs within large genomic sequences
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Recursive-iterative-DCM3
for large scale phylogeny reconstruction
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Probalign
for multiple sequence alignment
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Sdiscover:
finding active motifs in a set of protein or DNA
sequences
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RSmatch/RADAR: aligning RNA secondary structures
and finding RNA motifs
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