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ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well as application development. ProDy also comes with several analysis applications and a graphical user interface for visual analysis.

You can run ProDy on all major platforms. For download and installation instructions see:

• http://prody.csb.pitt.edu/downloads

• Homepage: http://prody.csb.pitt.edu/
• Tutorials: http://prody.csb.pitt.edu/tutorials
• Reference: http://prody.csb.pitt.edu/manual
• Applications: http://prody.csb.pitt.edu/manual/apps
• NMWiz GUI: http://prody.csb.pitt.edu/nmwiz
• Changes: http://prody.csb.pitt.edu/manual/release

• Source code: https://github.com/prody/ProDy
• Issue tracker: https://github.com/prody/ProDy/issues

ProDy is available under MIT License. See LICENSE.txt for more details.

Biopython (http://biopython.org/) KDTree and pairwise2 modules are distributed with ProDy. Biopython is developed by The Biopython Consortium and is available under the Biopython license (http://www.biopython.org/DIST/LICENSE).

Pyparsing (https://github.com/pyparsing/pyparsing) module is distributed with ProDy. Pyparsing is developed by Paul T. McGuire and is available under the MIT license (http://www.opensource.org/licenses/mit-license.php).

CEalign module (https://pymolwiki.org/index.php/Cealign_plugin) is distributed with ProDy. The original CE method was developed by Ilya Shindyalov and Philip Bourne. The Python version which is used by ProDy is developed by Jason Vertrees and available under the New BSD license.