MODENA (for multiple targets) website



MODENA (Multi-Objective DEsign of Nucleic Acids) is an inverse folding program based on multi-objective genetic algorithm. Non profit, academic users can download and use MODENA. For non-academic or commercial use, please contact the author.
Copyright(C) 2014, Akito Taneda Laboratory.



The follwing gipped files include an executable file and a pdf manual.

Linux 64 bit (x86_64)
Linux 32 bit (i686)
Mac OS X (10.9)

We have tested these files with CentOS 5 & 6 (x86_64), Ubuntu 12 (x86_64), Ubuntu 13 (i686), and Mac OS 10.9. Please read the manual in the downloaded files (Windows version is currently in progress) .

Currently, I would like to distribute executable files alone.

NOTE1 for the Mac version: If user would like to utilize the Fold program of RNAstructure package as method, the full path of the Fold program has to be specified (see, if a program named 'fold' has already been installed in Mac OS X.

NOTE2 for the Mac version: NUPACK, UNAFold, and RNAsoft packages and FindPath cannot be used as methods of MODENA. Parallelization (OpenMP) also cannot be used .

Target structure files used in the paper


The following gipped file includes readme.txt in which example MODENA commands are written.

input files for MODENA



Akito Taneda, Multi-objective optimization for RNA design with multiple target secondary structures, BMC Bioinformatics 16:280 (2015).(pubmed) (Correction in Table 5: "d and e indicate ..." -> "e and d indicate ...").

Akito Taneda, MODENA: a multi-objective RNA inverse folding, Adv. Appl. Bioinform. Chem. 4: 1-12 (2011). (pubmed)

Akito Taneda, Multi-objective genetic algorithm for pseudoknotted RNA sequence design, Front. Genet. 3:36 (2012). (pubmed) (supplementary material)

Comments, bug reports are welcome. E-mail: taneda (at)