RNAStructAlignmentML is a format for storing rna secondary structure alignments as computed by e.g. the RNAforester {http://bibiserv.techfak.uni-bielefeld.de/rnaforester} or RNAalifold {http://www.tbi.univie.ac.at/~ivo/RNA/} tool. RNAStructAlignment uses a RNAStructML-like architecture, but uses AlignmentML instead of SequenceML as a basic type. this element contains rna secondary structure alignment information along with sequence and program information optional version tag this type can contain rna secondary structure alignment information along with sequence and program information element for storing program/tool information e.g. command line calls represents a rna structure alignment element for storing sequence data. two sequences are required, since an alignment over one sequence does not make sense this element can contain a comment this element can contain consensus data for the alignment score value can contain identifier type describing sequence data for rna secondary structure alignments. inspired by AlignmentML. name of the sequence synonyms for the name sequence description element for storing aligned nucleotid sequences element for storing unrestricted aligned sequences empty sequence element element for storing rna secondary structure alignment belonging to the sequence optional comment mandatory sequence identifier inherit gappedFreeSequenceType from hobitTypes; does not allow gaps An aligned nucleic acid sequence. type for containing rna secondary structure alignments energy value probability value type for containing rna secondary structure alignment consensus data consensus rna secondary structure structure probabilities consensus sequence optional identifier type for consensus sequences probability list describing consensus sequence probabilities probability list describing consensus sequence probabilities simple type for probabilities Defines a list of structure probabilities, which is a triplet of two positions and and a probability. Defines a new type for structure probability. A structure probability is defined by two bases and a pairing probability between them. Position of the first base. Position of the second base. Probability of the base pair.