Cosine similarity, Clustering and Phylogeny

[bonfaceonyango]

Exploration of cosine similarity, hierarchical clustering, and phylogeny

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[Shuyib]

Thank you for this. I am testing each section using Codespaces and different py environments to ensure everything works correctly. Find the comments about the sections of the pull request below. Sorry to keep you waiting.

• [x] added more libraries
  • [x] works in Codespaces
  • [x ] In different py versions set (will be confirmed with CI/CD)
    • [x] cosine similarity exploration
      • [x] fix typos
      • [x] add make run_script command to notebook
      • [x] Update py files to accomodate 9mers
      • [x] Update the orientation of plots to horizontal to see the terminal nodes clearly
      • [x] Swap out the axes
      • [x] Update section to add 9mer trees
    • [x] newick representation of the dendogram clusters.