Evol Tutorial

You can also read this tutorial in PDF format.

• Introduction
  • Required Programs
  • Recommended Programs
  • Getting Started
• Pfam Access
  • Search Pfam
  • Retrieve MSA files
• MSA Files
  • Parsing MSA files
  • Filtering and Slicing
  • MSA objects
  • Merging MSAs
  • Writing MSAs
• Evolution Analysis
  • Get MSA data
  • Refine MSA
  • Occupancy calculation
  • Entropy Calculation
  • Mutual Information
  • Output Results
  • Rank-ordering
• Sequence-Structure Comparison
  • Entropy Calculation
  • Mobility Calculation
  • Comparison of mobility and conservation
  • Writing PDB files
• Evol Application

Acknowledgments

Continued development of Protein Dynamics Software ProDy and associated programs is partially supported by the NIH-funded R01 GM139297 entitled “Toward a deeper understanding of allostery and allotargeting by computational approaches”.