<em>Partition Function (-p)</em><br /> Calculate the Partition
Function and base pairing probability matrix in addition to the mfe
structure. A coarse representation of the pair probabilities in the
<em>Partition Function (-p)</em><br /> Calculate the Partition
Function and base pairing probability matrix in addition to the mfe
structure. A coarse representation of the pair probabilities in the
derived from the pair probabilities are displayed. The most likely
base pairings are stored in a separate file by RNAalifold and
represented in Jalview by a bar graph annotation line labeled
derived from the pair probabilities are displayed. The most likely
base pairings are stored in a separate file by RNAalifold and
represented in Jalview by a bar graph annotation line labeled