RNAsoup (Spot grOUPs in RNA cluster-tree) is a post-processing tool of a structural clustering pipeline for structured RNAs (e.g. RNAclust). It requires as input a binary cluster-tree, the minimum free energy (MFE) of the consensus secondary structure for each internal node, and a FASTA file of the input sequences. It detects the optimal partition (i.e. finding the optimal number of clusters/groups) into distinct subtrees where each subtree contains structurally related RNA sequences. RNAsoup is based on a decision rule which evaluates the squared error from the minimum free energies of the single sequences to the minimum free energy of the consensus secondary structure.
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