For computationally intensive tasks you may consider downloading the standalone version of SupeRNAlign.
The latest version can be obtained from BitBucket repository:
Download SupeRNAlign (.zip file)
Please keep in mind that you need to install an older version of R3D Align (available here) in order to use it with SupeRNAlign.A detailed tutorial is available.
Laboratory of Bioinformatics and Protein EngineeringTrojdena 4, 02-109 Warsaw, POLAND