CONTRAfold is available as open source software under the BSD license. CONTRAfold 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.

• Source code (C++): This version of the code contains a number of minor speed improvements over 2.00.


• A manual describing how to use the CONTRAfold program.

• v2.00 source code (C++): This is a complete reimplementation of core parts of the CONTRAfold inference engine. This version of the code is far faster than v1.10. Model parameters were trained using the S-Processed dataset, available here.
• v1.00 source code (C++)


• A manual describing how to use the CONTRAfold program.
• A technical note describing the recurrences needed to implement the CONTRAfold model.


• A C++ program for scoring a test BPSEQ file against a reference BPSEQ file.
• A C++ program for generating BPSEQ format training set from Rfam (version 7.0) seed alignments.
• An archive containing automatically selected Rfam sequences, partitioned into two folds (A and B).
• An archive containing structures above, with all pseudoknots removed.