This file defines the top-level module for the Cassiopeia tree solver package. It imports and exposes various solver classes and dissimilarity functions for phylogenetic tree reconstruction.
This file simply imports various solver classes and a module containing dissimilarity functions. These classes and functions are used by other modules in the Cassiopeia solver package.
A hybrid solver that combines a top-down greedy algorithm with a more complex bottom-up solver. The greedy solver is applied until a certain criteria is reached (e.g., maximum LCA distance or number of cells), after which the bottom solver is used to reconstruct subproblems.
A solver that uses a max-cut heuristic to partition samples based on a connectivity graph representing a supertree of phylogenetic trees on each individual character.
A solver that implements a variation of the Spectral Neighbor-Joining algorithm to iteratively join subsets of leaves into a cherry based on the second singular value of the RA matrix.
