R-scape - RNA Structural Covariation Above Phylogenetic Expectation http://eddylab.org/R-scape/
R-scape looks for evidence of a conserved RNA structure by measuring pairwise covariations observed in an input multiple sequence alignment. It analyzes all possible pairs, including those in your proposed structure (if you provide one). R-scape uses a null hypothesis that takes phylogenetic correlations and base composition biases into account, which can be sources of apparent pairwise covariation that are not due to conserved RNA structure. R-scape also estimates the statistical power to detect a significantly covarying base pair when that much variation is present. R-scape can calculate a structure based on the observed covariations using the CaCoFold algorithm.
Other files to read in the top-level source directory:
INSTALL Brief installation instructions.
documentation/R-scape_userguide.pdf The R-scape User's Guide.
LICENSE copyright and license information
To get started after installation, see the tutorial section in the R-scape User's Guide (documentation/R-scape_userguide.pdf).
The R-scape development team github.com/EddyRivasLab/RivasLab/R-scape/ http://eddylab.org/R-scape