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Virtual Machines with Galaxy/NanoTiler pipeline, RNA2D3D, and StructureLab installed - (2017-2021)

Preconfigured Virtual Machine appliance files (full system in one file) for the Oracle's free VirtualBox with Ubuntu LTS versions or CentOS Linux and local Galaxy server with NanoTiler pipeline, RNA2D3D, and StructureLab. These provide the most covenient way to sample several of our tools without the effort needed to resolve library dependencies that may differ between Linux flavors.

RiboSketch - (2018)

A multi-strand molecule drawing web server. [Online Version]

CovaRNA (C++ sources) and CovStat (R package)

The CovaRNA and CovStat software packages for detecting long-range covariations in nucleotide alignments. This is the software corresponding to the publication of Bindewald and Shapiro: Computational detection of abundant nucleotide-covariation in Drosophila genomes. RNA, 2013. [Publication] | [Pubmed]


A Java application for the design of RNA nanoscale structures from building blocks.


A C++ application (sources and 64bin Linux binaries) for a stand-alone version of our CorreLogo server for the 3D sequence logos of RNA and DNA. [Online Version]


Single sequence RNA secondary structure prediction, including pseudoknots. [Online Version]


KNetFold is a new software for predicting the consensus secondary structure for a given alignment of RNA sequences. [More Information] | [Online Version]

RSMatch 2.0

A package for comparing RNA structures via 1) pair-wise and DB searches; 2) multiple structure alignment with common structure computation; 3)iterative DB searches.


An interactive system for the conversion of RNA 2D structures to 3D and 3D modeling.


An RNA workbench that assists in the 2D structure elucidation (with limited 3D capabilities). [More Information]


A massively parallel genetic algorithm that predicts RNA secondary structure. [More Information]
Please note: To obtain a copy of this software contact Dr. Bruce A. Shapiro directly.

MPGAfold Visualizer

A Java application that allows the user to visually see an MPGAfold run. [More Information]
Please note: To obtain a copy of this software contact Dr. Bruce A. Shapiro directly.

Note that not all of our software is available for download. If you cannot find the package you are looking for here, please, contact