Ambiguous greedy & parallel dissimilarity computation

.gitignore

@@ -165,5 +165,4 @@ stdout.log
 notebooks/.ipynb_checkpoints
 cassiopeia/tools/branch_length_estimator/_iid_exponential_bayesian.cpp
 docs/api/reference/**
-cassiopeia/config.ini
 .vscode

cassiopeia/data/CassiopeiaTree.py

@@ -1401,7 +1401,11 @@ def get_mutations_along_edge(
 
         mutations = []
         for i in range(self.n_character):
-            if parent_states[i] != child_states[i]:
+
+            parent_state = (list(parent_states[i]) if is_ambiguous_state(parent_states[i]) else [parent_states[i]])
+            child_state = (list(child_states[i]) if is_ambiguous_state(child_states[i]) else [child_states[i]])
+
+            if len(np.intersect1d(parent_state, child_state)) < 1:
                 if treat_missing_as_mutations:
                     mutations.append((i, child_states[i]))
                 elif (
@@ -1828,6 +1832,7 @@ def compute_dissimilarity_map(
         ] = None,
         prior_transformation: str = "negative_log",
         layer: Optional[str] = None,
+        threads: int = 1
     ) -> None:
         """Computes a dissimilarity map.
 
@@ -1854,6 +1859,7 @@ def compute_dissimilarity_map(
                         the square root of 1/p
             layer: Character matrix layer to use. If not specified, use the
                 default :attr:`character_matrix`.
+            threads: Number of threads to use for dissimilarity map computation.
         """
 
         if layer is not None:
@@ -1884,6 +1890,7 @@ def compute_dissimilarity_map(
             dissimilarity_function,
             weights,
             self.missing_state_indicator,
+            threads=threads,
         )
 
         dissimilarity_map = scipy.spatial.distance.squareform(dissimilarity_map)