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the-protein-engineering-tournament / pet-pilot-2023

Results and data from the pilot round of the Protein Engineering Tournament
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MDS analysis plot #10

Closed ryamy closed 2 days ago

ryamy commented 1 month ago

Thanks for your great work! I found the MDS analysis plot on Fig. 4, could you show us the code of MDS analysis? I think this plot is very useful , and I would like to create same plot on my own data. I am just interested in how to create distance matrix represent sequence distance and number of mutations simultaneously.

hredestig commented 2 days ago

Thanks for patience with slow reply. Here's the code for the MDS plot https://github.com/debbiemarkslab/sequenceMDS/blob/main/sequenceMDS%20example%202%20-%20alignbio%20tournament%202023.ipynb