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matsengrp / larch

Inference and manipulation of history DAGs
MIT License
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Summary of goals #36

Open willdumm opened 1 year ago

willdumm commented 1 year ago

This issue can serve as a summary of our goals for Larch, approximately in the order of priority/practicality

  1. adding all edges #23
  2. practical trimming/subsetting efficiently, especially to explore trimming in larch-usher #14
  3. New weights, such as shifted sum RF distance #29
  4. Sampling proportional to weights (especially sum RF distance, parsimony) #29
  5. leaf ambiguities (discussed https://github.com/matsengrp/historydag/issues/38 and #37)
  6. optimizing subtrees / make optimization faster #33
  7. Optimizing on huge dags #40
  8. Direct dag optimization or modification by callback #6