Citation

Meyer IM, Miklós I. (2007) SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput Biol. 2007 Aug;3(8):e149. doi: 10.1371/journal.pcbi.0030149

Download Program

• SimulFold tar-ball (see included COPYRIGHT file), or clone our git repository
• use "java SimulFold alignment_file tree_file -S -T -A" to execute the program locally and to sample alignments (A), trees (T) and structures (S)
• please note that input trees on the command line have to be binary, rooted trees in Newick format
• bp2bistruc tar-ball required to parse output

Manuscript Data

• CARNAC input and output files (tar-ball)
• HXMATCH input and output files (tar-ball)
• Pfold input and output files (tar-ball)
• RNAalifold input and output files (tar-ball)
• SimulFold input and output files (tar-ball)
• SimulFold raw output files (LARGE tar-ball 4.5MB)

Disclaimer

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.