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Lots of branches from old issues that could be deleted #115

Description

@WilliamZekaiWang

notably ones that have closed issues but still have branches:

  • iss32
  • iss48
  • iss49
  • iss64

This is for #93, which has been referenced as solved in #101

  • iss93

This is branch is for #94 which we can't really do because we haven't located a direct solution to accessing 3seq functions to lock one parent sequence

  • iss94

Ones still relevant

  • iss100 (RDP refactoring)
  • maxchi_chimera (maxchi and chimera refactoring)
  • siscan (siscan refactoring, also includes upgma)

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