Prune negative branch lengths from rapidnj

bacpop · Apr 28, 2020 · 3381148 · 3381148
1 parent ca0abea
commit 3381148
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/PopPUNK/plot.py b/PopPUNK/plot.py
@@ -594,7 +594,7 @@ def buildRapidNJ(rapidnj, refList, coreMat, outPrefix, tree_filename):
             pFile.write("\n")
 
     # construct tree
-    rapidnj_cmd = rapidnj + " " + phylip_name + " -i pd -o t -x " + tree_filename + ".raw"
+    rapidnj_cmd = rapidnj + " " + phylip_name + " -n -i pd -o t -x " + tree_filename + ".raw"
     try:
         # run command
         subprocess.run(rapidnj_cmd, shell=True, check=True)