RAF is a program for multiple RNA alignment and folding. Given a set of homologous, unaligned RNA sequences, RAF compute a multiple alignment and consensus structure prediction using a progressive simultaneous alignment and folding algorithm.

RAF is available as open source software under the BSD license. RAF was developed on Ubuntu Linux 7.10. The source code is known to compile correctly using the GCC 4.1.3 C++ Compiler. If you have any trouble compiling or running the software on your system, please let us know.

• v1.00 source code (C++)
  
• A manual describing how to use the RAF program.

• Do, C.B., Foo, C.-S., and Batzoglou, S. (2008) A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics 24: i68-i76.