diff --git a/lshmm/core.py b/lshmm/core.py
index e912959..137a8bc 100644
--- a/lshmm/core.py
+++ b/lshmm/core.py
@@ -322,14 +322,14 @@ def get_emission_probability_haploid_hkylike(ref_allele, query_allele, site, emi
         raise ValueError("Reference allele cannot be MISSING.")
     if query_allele == NONCOPY:
         raise ValueError("Query allele cannot be NONCOPY.")
-    if emission_matrix.shape[1] != 2:
+    if emission_matrix.shape[1] != 4 or emission_matrix.shape[2] != 4:
         raise ValueError("Emission probability matrix has incorrect shape.")
     if ref_allele == NONCOPY:
         return 0.0
     elif query_allele == MISSING:
         return 1.0
     else:
-        return emission_matrix[ref_allele, query_allele]
+        return emission_matrix[site, ref_allele, query_allele]
 
 
 @jit.numba_njit
@@ -343,22 +343,25 @@ def get_emission_matrix_hkylike(mu, kappa=None):
     :param float mu: Probability of mutation to any allele.
     :param float kappa: Transition-to-transversion rate ratio.
     """
-    if kappa <= 0:
-        raise ValueError("Ts/tv ratio must be positive.")
-    # Assume that ACGT are encoded as 0 to 3.
-    num_alleles = 4
-    emission_matrix = np.zeros((num_alleles, num_alleles), dtype=np.float64) - 1
-    for i in range(num_alleles):
+    if kappa is not None:
+        if kappa <= 0:
+            raise ValueError("Ts/tv ratio must be positive.")
+    num_sites = len(mu)
+    num_alleles = 4 # Assume that ACGT are encoded as 0 to 3.
+    emission_matrix = np.zeros((num_sites, num_alleles, num_alleles), dtype=np.float64) - 1
+    for i in range(num_sites):
         for j in range(num_alleles):
-            if i == j:
-                emission_matrix[i, j] = 1 - mu
-            else:
-                emission_matrix[i, j] = mu / 3
-                if kappa is not None:
-                    # Transitions: A <-> G, C <-> T.
-                    is_transition = (i in [0, 2] and j in [0, 2]) or (i in [1, 3] and j in [1, 3])
-                    if is_transition:
-                        emission_matrix[i, j] *= kappa
+            for k in range(num_alleles):
+                if j == k:
+                    emission_matrix[i, j, k] = 1 - mu[i]
+                else:
+                    emission_matrix[i, j, k] = mu[i] / 3
+                    if kappa is not None:
+                        # Transitions: A <-> G, C <-> T.
+                        is_transition_AG = i in [0, 2] and j in [0, 2]
+                        is_transition_CT = i in [1, 3] and j in [1, 3]
+                        if is_transition_AG or is_transition_CT:
+                            emission_matrix[i, j, k] *= kappa
     return emission_matrix