RNAalifold is part of the Vienna RNA Secondary Structure Prediction and Comparison Package. It was described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler, RNAalifold: Improved consensus structure prediction for RNA alignments. (BMC Bioinformatics, 9:474, 2008).

Example RNAalifold Output
RNAalifold prints a consensus alignment and mfe structure to stdout with its associated energy. Depending on the arguments given, other information such as alternate structures are displayed below while base pairing probabilities (-p or --MEA options) are stored in a separate 'alifold.out' file.

G_UUUCAUU___AUGACGGCCUGUGCU_UAAA__CCUCC____GAG__C________GGGUCA_G_G_UCUGAU___CUUG_______GAGAC
(.((((...........(((((((((........(((......)))............))))).).).))..................))))) (-19.16 = -11.80 +  -7.36) 
(.((((...........(((((((((........(((......)))............))))).).).))..................))))) [-19.32]
	frequency of mfe structure in ensemble 0.765639
(.((((...........(((((((((........(((......)))............))))).).).))..................))))) -19.16 {-11.80 +  -7.36}
(.((((...........(((((((((........(((......)))............))))).).).))..................))))) { 13.20 MEA=92.14}

Alifold.out
   	6    89  9  99.2%   0.023 CG:29   GC:14   UA:9   
   	4    91 11  99.1%   0.028 CG:20   GC:11   UG:2    UA:17  
   	3    92 18  96.9%   0.090 CG:5    GC:2    GU:1    UG:4    AU:6    UA:25  
  	35    46  3  93.3%   0.195 CG:31   GC:16   UG:2    AU:5    UA:4   
  	36    45 10  93.6%   0.185 CG:16   GC:6    GU:1    UG:2    AU:8    UA:18  
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Running RNAalifold from Jalview
To run RNAalifold go to Webservices→RNA Structure Prediction and choose RNAalifold Defaults to run with no arguments or edit settings and run ... to adjust the parameters before running. Details of all the RNAalifold parameters can be found in the RNAalifold Manpage. JABAWS and Jalview support a selection of the RNAalifold arguments only.

Supported Arguments which give alternate structures

Partition Function (-p)
Calculate the Partition Function and base pairing probability matrix in addition to the mfe structure. A coarse representation of the pair probabilities in the from of a psuedo bracket notation, as well as the centroid structure 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 labelled 'Contact Probabilities'.

Maximum Expected Accuracy Structure (--MEA)
Calculate an MEA structure where the expected Accuracy is computed from the base pair probabilities. A more detailed description is found in the RNAfold documentation.

Example RNAalifold Structure Annotation rows