Fix distance matrix

metagenopolis · Nov 26, 2024 · 33284a2 · 33284a2
1 parent d1e364e
commit 33284a2
Showing 1 changed file with 4 additions and 3 deletions.
diff --git a/meteor/phylogeny.py b/meteor/phylogeny.py
@@ -175,11 +175,12 @@ def process_msp_file(
             if self.gtr:
                 d = EstimateDistances(aligned_seqs, submodel=GTR())
                 d.run(show_progress=False)
+                # Create UPGMA Tree
+                mycluster = upgma(d.get_pairwise_distances())
             else:
-                d = aligned_seqs.distance_matrix(calc="tn93", show_progress=False)
+                dists = aligned_seqs.distance_matrix(calc="tn93", show_progress=False)
+                mycluster = upgma(dists)
 
-            # Create UPGMA Tree
-            mycluster = upgma(d.get_pairwise_distances())
             mycluster = mycluster.unrooted_deepcopy()
 
             with tree_file.open("w") as f: