diff --git a/parsnp b/parsnp
index 9501ab8..2a3e535 100755
--- a/parsnp
+++ b/parsnp
@@ -25,7 +25,7 @@ from pathlib import Path
 import extend as ext
 from tqdm import tqdm
 
-__version__ = "2.0.2"
+__version__ = "2.0.3"
 reroot_tree = True #use --midpoint-reroot
 random_seeded = random.Random(42)
 
@@ -1452,6 +1452,7 @@ SETTINGS:
         ref = auto_ref
 
     finalfiles = sorted(finalfiles)
+    random_seeded.shuffle(finalfiles)
     totseqs = len(finalfiles)
 
     #initiate parallelPhiPack tasks