diff --git a/modisco/core.py b/modisco/core.py
index af476ae..9886ee0 100644
--- a/modisco/core.py
+++ b/modisco/core.py
@@ -774,7 +774,7 @@ def compute_subclusters_and_embedding(self, pattern_comparison_settings,
         distmat_sp.sort_indices()
         if (compute_embedding):
             twod_embedding = sklearn.manifold.TSNE(
-                perplexity=perplexity,
+                perplexity=min(perplexity, distmat_sp.shape[0]),
                 metric='precomputed',
                 init="random",
                 verbose=3, random_state=1234).fit_transform(distmat_sp) 
diff --git a/setup.py b/setup.py
index 24273fc..ec33249 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
           description='TF MOtif Discovery from Importance SCOres',
           long_description="""Algorithm for discovering consolidated patterns from base-pair-level importance scores""",
           url='https://github.com/kundajelab/tfmodisco',
-          version='0.5.16.3',
+          version='0.5.16.4',
           packages=find_packages(),
           package_data={
                 '': ['cluster/phenograph/louvain/*convert*', 'cluster/phenograph/louvain/*community*', 'cluster/phenograph/louvain/*hierarchy*']