Summary of goals

[willdumm]

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

1. adding all edges Add all possible edges #23
2. practical trimming/subsetting efficiently, especially to explore trimming in larch-usher Trimming the DAG #14
3. New weights, such as shifted sum RF distance Sampling from the DAG's topological fringe #29
4. Sampling proportional to weights (especially sum RF distance, parsimony) Sampling from the DAG's topological fringe #29
5. leaf ambiguities (discussed Support for leaf labels with ambiguities historydag#38 and Ambiguous Samples #37)
6. optimizing subtrees / make optimization faster Larch-usher: optimize only a subtree at a time #33
7. Optimizing on huge dags Benchmarking on very large DAGs #40
8. Direct dag optimization or modification by callback Apply individual matOptimize moves to the DAG #6