diff --git a/run_gubbins.py b/run_gubbins.py
index fe3e6d9c..027423ad 100755
--- a/run_gubbins.py
+++ b/run_gubbins.py
@@ -233,7 +233,7 @@ def is_exe(fpath):
     if i == 1:
       previous_tree_name    = fasttree_previous_tree_name(base_filename, i)
       current_tree_name     = fasttree_current_tree_name(base_filename, i)
-      tree_building_command = fasttree_tree_building_command(i, args.starting_tree,current_tree_name,base_filename,previous_tree_name,FASTTREE_EXEC,'-fastest' )
+      tree_building_command = fasttree_tree_building_command(i, args.starting_tree,current_tree_name,base_filename,previous_tree_name,FASTTREE_EXEC, FASTTREE_PARAMS )
       gubbins_command       = fasttree_gubbins_command(base_filename,starting_base_filename+".gaps", i,args.alignment_filename,GUBBINS_EXEC,args.min_snps)
       
     elif i == 2: