PhyloRNAalifold is a program for predicting consensus structures of aligned RNA sequences by incorporating phylogetetic-based covarying mutations.
The implementation of PhyloRNAalifold is on the top of RNAalifold  from the Vienna RNA Package v2.0 . Vienna RNA Package is developed by the Institute for Theoretical Chemistry of the University of Vienna.
USAGE: PhyloRNAalifold [-r] [--cfactor=DOUBLE] [--nfactor=DOUBLE] infile treefile [beta]
- infile : a ClustalW format file containg a multiple sequence alignment of related RNAs.
- treefile: a Newick tree format file containing the phylogenetic tree of the alingment in infile. Only rooted binary tree is accepted.
- beta: a parameter in the PhyloRNAalifold algorithm. Its default value is 10.
- -r: use ribosum scoring matrix.
- --cfactor: set the weight of the covariance term in the energy function.
- --nfactor: set the penalty for non-compatible sequences in the covariance term of the energy function.
- *Note: All the other command line arguments of RNAalifold are contained in PhyloRNAalifold, but on solid testing is performed on them. Some arguments may cause run time problems.
- Benchmarking dataset is available here.
Ge, P., Zhang, S. (2013) Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction. BMC Bioinformatics, 14:142. (Full Text)
- PhyloRNAalifold v1
*Copyright: PhyloRNAalifold is free for research, educational, commercial use and modification.
Credits should also be given to RNAalifold (Ivo Hofacker's group) if the software is used.
 Hofacker, I. L., Fekete, M., & Stadler, P. F. (2002) Secondary structure prediction for aligned RNA sequences. Journal of molecular biology, 319(5), 1059-1066.
 Vienna RNA Package, RNA Secondary Structure Prediction and Comparison. http://www.tbi.univie.ac.at/RNA/
Please contact Shaojie Zhang if you have any suggestions.