ccphylo_solver_test.py
: Tests CCPhylo solver implementationsdissimilarity_functions_test.py
: Tests dissimilarity and similarity functionsgreedy_variants_test.py
: Tests variants of the greedy solver algorithmhybrid_solver_test.py
: Tests the hybrid solver combining multiple algorithmsilp_solver_test.py
: Tests the Integer Linear Programming solvermaxcut_test.py
: Tests the MaxCut solverneighborjoining_solver_test.py
: Tests the Neighbor Joining solverpercolation_test.py
: Tests the Percolation solversharedmutationjoiner_test.py
: Tests the Shared Mutation Joining solversnj_solver_test.py
: Tests the Spectral Neighbor Joining solverspectral_test.py
: Tests the Spectral solverupgma_test.py
: Tests the UPGMA solvervanillagreedy_test.py
: Tests the Vanilla Greedy solverunittest.TestCase
and includes multiple test methods covering different aspects of the respective solver or utility.
neighborjoining_solver_test.py
: Tests the widely-used Neighbor Joining algorithmilp_solver_test.py
: Tests the Integer Linear Programming solver, which can provide optimal solutions for smaller datasetsdissimilarity_functions_test.py
: Tests critical dissimilarity and similarity functions used across multiple solvershybrid_solver_test.py
: Tests the hybrid solver that combines multiple algorithms, representing a more advanced approachconfig.ini
file and a ccphylo_path
setting.find_triplet_structure
, to assist in verifying tree structures and comparing results across different solvers.
In summary, this test suite provides comprehensive coverage of the phylogenetic tree reconstruction algorithms implemented in Cassiopeia, ensuring their correctness and reliability across a wide range of scenarios and input conditions.