diff --git a/src/aniclustermap/cluster.py b/src/aniclustermap/cluster.py
index 3c2e401..fede665 100644
--- a/src/aniclustermap/cluster.py
+++ b/src/aniclustermap/cluster.py
@@ -8,6 +8,7 @@
 import seaborn as sns
 from matplotlib.colors import BoundaryNorm
 from matplotlib.colors import LinearSegmentedColormap as LSC
+from scipy.spatial.distance import squareform
 from seaborn.matrix import ClusterGrid
 
 
@@ -59,7 +60,7 @@ def clustermap(
         ani_matrix_df = pd.read_csv(ani_matrix_df, sep="\t", encoding="utf-8")
 
     if linkage is None:
-        linkage = hc.linkage(ani_matrix_df, method="average")
+        linkage = hc.linkage(squareform(100 - ani_matrix_df), method="average")
 
     if cmap_colors is None:
         cmap_colors = ["lime", "yellow", "red"]
diff --git a/src/aniclustermap/scripts/aniclustermap.py b/src/aniclustermap/scripts/aniclustermap.py
index b751f07..10c80b5 100644
--- a/src/aniclustermap/scripts/aniclustermap.py
+++ b/src/aniclustermap/scripts/aniclustermap.py
@@ -9,6 +9,7 @@
 import pandas as pd
 import scipy.cluster.hierarchy as hc
 import typer
+from scipy.spatial.distance import squareform
 from typer import Option, Typer
 
 from aniclustermap import __version__, const
@@ -172,7 +173,7 @@ def cli(
 
     # Hierarchical clustering ANI matrix
     logger.info(f"Clustering {mode.value} ANI matrix by scipy UPGMA method")
-    linkage = hc.linkage(ani_matrix_df, method="average")
+    linkage = hc.linkage(squareform(100 - ani_matrix_df), method="average")
     dendrogram_newick_file = outdir / "ANIclustermap_dendrogram.nwk"
     to_newick_tree(ani_matrix_df, linkage, dendrogram_newick_file)
     logger.info("Write newick format cluster dendrogram")