Circles is an experimental program for inferring RNA secondary structure using the comparative method. It provides a user-friendly interface to Jack Tabaska’s maximum weight matching programs. The user can read in an alignment in FASTA, Clustal, or NEXUS format, compute a maximum weight matching, and export one or more secondary structures in standard formats.
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Circles: automating the comparative analysis of RNA secondary structure
Bioinformatics (2000) 16 (11): 1042-1043.