diff --git a/lshmm/api.py b/lshmm/api.py
index d6d662d..0e4a3a8 100644
--- a/lshmm/api.py
+++ b/lshmm/api.py
@@ -239,6 +239,7 @@ def forwards(
         emission_matrix,
         prob_recombination,
         norm=normalise,
+        emission_func=core.get_emission_probability_haploid,
     )
 
     return forward_array, normalisation_factor_from_forward, log_lik
@@ -279,6 +280,7 @@ def backwards(
         emission_matrix,
         normalisation_factor_from_forward,
         prob_recombination,
+        emission_func=core.get_emission_probability_haploid,
     )
 
     return backwards_array
@@ -313,6 +315,7 @@ def viterbi(
             query_checked,
             emission_matrix,
             prob_recombination,
+            emission_func=core.get_emission_probability_haploid,
         )
         best_path = backwards_viterbi_hap(num_sites, V, P)
     else:
@@ -323,6 +326,7 @@ def viterbi(
             query_checked,
             emission_matrix,
             prob_recombination,
+            emission_func=core.get_emission_probability_diploid,
         )
         unphased_path = backwards_viterbi_dip(num_sites, V, P)
         best_path = get_phased_path(num_ref_haps, unphased_path)
@@ -365,6 +369,7 @@ def path_loglik(
         query_checked,
         emission_matrix,
         prob_recombination,
+        emission_func=core.get_emission_probability_haploid,
     )
 
     return log_lik