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Welcome to the DyNoPy tutorial!

Hopefully, you will find the instructions provided here useful on how to use this code.

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Listed below are the sequence of steps on how to generate the J-matrix and extract the community of residues collectively contributing to the dynamics of interest.

Step 0. Description of dynamics

Step 1. Coevolution analysis.

Step 2. Calculate Pairwise interaction energies

Step 3. Calculate Rho matrix

Step 4. Calculate J matrix

Step 5. Network analysis

Step 6. Visualisation

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General tips

You can invoke the help by using the -h flag. eg:

dyno_coevolution.py -h

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