FledFold combines both thermodynamic and kinetic factors for RNA secondary structure and can predict RNA secondary structures from single primary sequences. Our early work has shown the accuracy of fledFold is higher than the accuracy of traditional methods, especially for RNAs without pseudoknots.


FledFold is implemented in C++ and it can be downloaded here. At present, fledFold can run on Windows 7, Windows 10, Windows Vista, Windows XP with 2 Gb of RAM at least.

Input & Output

FledFold requires input FASTA files under the path 'fledFold/sequences'. These FASTA files must be named in English, and the length of each name should less than 90 characters. If the number of FAST file is no more than 1000, fledFold will process all the all the FASTA files one by one once it is launched, otherwise, fledFold will only process the first 1000 FASTA files.

The outcome of Fledfold are presented in dot-parenthesis format, Connectivity Table (CT) file and Scalable Vector Graphics (SVG) format with the same name as the corresponding input FASTA file. Note that if there is a file with the same as the output file of fledFold, this file will be overwritten by fledFold.

How to use fledFold

  1.Down fledFold software package freely at here.

  2.Use any unzip software to extract the package.

  3.Put the sequence files under the path fledFold/sequences/.

  4.Run the fledFold/fledFold.exe in command line or double click the fledFold.exe.

  5.Check the outcome files under the path fledFold/sequences/.


If any mistake below is made, fledFold will prompt the mistake or stop running.

  1.The length of FASTA file name is more than 90 characters.

  2.The number of FASTA files is more than 1000.

  3.Invalid character in the FASTA file.

  4.Invalid format of FASTA file.

  5.Remove or rename the folder 'sequence'.

Contact us

FledFold is under continuous development. If you have any question or the find bugs in this program, please contact us (mianfeiyouxiangzq@163.com). we would value your feedback with suggestions and improvements.


FledFold was written by Qi Zhao. This software is freely available for academic or non-commercial purpose. Any usage of fledFold may cite the reference Liu Y, Zhao Q, Zhang H, et al. A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation[J]. 2015.