PPfold

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LAST UPDATE: May, 2014 (New release: version 3.1.1)

PPfold is a new implementation of pfold, written in Java 6.0. It can predict the consensus secondary structure of RNA alignments through a stochastic context-free grammar coupled to an evolutionary model. It can also use data from chemical probing experiments to predict RNA secondary structure. PPfold is multithreaded, and can solve the structure of much longer alignments than pfold. It is also platform-independent and much more user-friendly than pfold. PPfold can be downloaded as a standalone program as well as a free plugin to the CLC Workbenches.

NEW RELEASE (May, 2014): PPfold version 3.1.1 Fixed a bug that caused PPfold to crash when trying to fold with particular hard constraints.

Licensing information:
PPfold is and will remain free software. If you find it useful, you can cite one of our publications. If you are into the formalities, PPfold is distributed under the 4-clause BSD license.
The CLC Workbench plugin is also free, but it uses the proprietary CLC Developer Kit API from CLC bio, a QIAGEN company.

If you experience any issues, or have questions or comments, email:

Zsuzsanna Sukosd (dsokus[at]gmail.com) (Note: as I no longer work at the university, new features are not expected to PPfold, but I will do my best to address any errors.)

Instructions and download links

PPfold (standalone):

Choose this if you just want to run the program as a standalone application:

Version 3.1.1 (current release): PPfold3.1.1.jar

(Old versions below.)

Given that you have Java installed on your computer, you can execute it

From the desktop (recommended): Simply double-click the file to start the program. (On some systems, you need to make the file executable first.) Select the input alignment (it must be in FASTA format). You can optionally also select a phylogenetic tree (in NEWICK format), and/or additional data tracks, eg. from chemical probing experiments. For file formats and examples, check out the Examples and FAQs page.
From the command line: type java -jar PPfold --help for information on command-line arguments and options, and check out the Examples and FAQs page for file formats and examples.

An advantage of using the PPfold GUI is that it will attempt to do a few checks on your data to look for obvious problems, before attempting to run the algorithm. The command-line version will only do limited checking.

PPfold (CLC plugin)

Choose this if you want to integrate it into a CLC Workbench:

PPfold is now an official (free) plugin to the CLC Workbenches. Please use the plugin site at CLC bio, a QIAGEN company, for download: PPfold at CLC bio

This will ensure that you always have the latest version compatible with your current installation. Instructions on how to use it can be also be found on CLC bio's website.

PPfold (source code, old versions and extras)

Choose this if you want to have a look at the source code, need the extra programs or want to use the old versions:

PPfold version 3.0 source code	PPfold3.0.zip
Extra C programs (from pfold)	pfold-extras.zip
PPfold version 3.0 binary (no longer maintained)	PPfold-v3-0.jar
PPfold version 2.0 binary (no longer maintained)	PPfold-v2-0.jar
PPfold version 1.0 binary (no longer maintained)	PPfold.jar
PPfold plugin version 1.0, CLC Workbench versions 5.x (no longer maintained)	PPfold.cpa
PPfold version 1.0 source	PPfold.zip
PPfold + CLC plugin integration version 1.0 source	PPfold-plugin.zip

Changelog

Current release, version 3.1.1

This is a small bugfix release.
Version 3.0

New features include support for data from chemical probing experiments (and other types of data), various bugfixes, and a MUCH better graphical user interface.
Version 2.0/2.01.

New features include maximum likelihood tree estimation, small bugfixes and a better user interface. Note changed command-line options (more UNIX-like than version 1.0)
Version 1.0. First release

Publications

Z. Sukosd, B. Knudsen, J. Kjems, C. N. S. Pedersen. PPfold 3.0: PPfold 3.0: Fast RNA secondary structure prediction using phylogeny and auxiliary data. Bioinformatics 28(16), 2012
Z. Sukosd, B. Knudsen, M. Vaerum, J. Kjems, E.S.Andersen. Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars BMC Bioinformatics 12:103, 2011

Project

PPfold has been created as part of the Collaborative Minigrid Project, in close cooperation between