autocorrelation_test.py
: Tests for spatial autocorrelation calculations.branch_length_estimator_tests/
: Directory containing tests for branch length estimation methods.coupling_test.py
: Tests for evolutionary coupling calculations.fitness_estimator_tests/
: Directory containing tests for fitness estimation methods.parameter_estimators_test.py
: Tests for parameter estimation functions.small_parsimony_test.py
: Tests for small parsimony algorithms.topology_test.py
: Tests for topology-related functions.tree_metrics_test.py
: Tests for various tree-based metrics and calculations.autocorrelation_test.py
: Tests the compute_morans_i
function for calculating Moran’s I statistic.branch_length_estimator_tests/
:
iid_exponential_bayesian_test.py
: Tests the IIDExponentialBayesian
estimator.iid_exponential_mle_test.py
: Tests the IIDExponentialMLE
estimator.coupling_test.py
: Tests the compute_evolutionary_coupling
function.fitness_estimator_tests/lbi_jungle_test.py
: Tests the Local Branch Index (LBI) fitness estimator.parameter_estimators_test.py
: Tests functions for estimating mutation rates and missing data probabilities.small_parsimony_test.py
: Tests Fitch-Hartigan algorithm and related parsimony functions.topology_test.py
: Tests topology-related functions, including cophenetic correlation calculations.tree_metrics_test.py
: Tests various tree-based metrics and likelihood calculations.unittest
: The standard Python unit testing framework.parameterized
: Used for creating parameterized tests.numpy
: Used for numerical operations and array manipulations.scipy
: Used for various scientific computing tasks, including numerical integration.networkx
: Used for working with graph structures, particularly in creating and manipulating tree topologies.pandas
: Used for data manipulation and analysis.cvxpy
: Used in optimization problems, particularly in the MLE branch length estimator.CassiopeiaTree
, IIDExponentialBayesian
, IIDExponentialMLE
, LBIJungle
, and others.