BayesFold's methods are applicable whenever there is a high probability that all the sequences in the input alignment fold into the same structure. For example, researchers studying sets of RNA sequences from closely related organisms and those using SELEX to find sequence families are likely to have data matching BayesFold's criterion.
Since BayesFold's method searches for an optimal structure to fit all sequences, alignments whose component sequences are unlikely to fold into the same structure are not good candidates for use with BayesFold. This is the case even when the sequences probably fold into a family of related structures. We hope to remove this limitation in future versions.