diff --git a/etc/run_clustalx b/etc/run_clustalx
index 0b9dd6a12ca5c35d9ceabaa84fd09fa201a48f17..d9ade6d1c3b804ac2bbed21b8f35484c93d6378b 100755
--- a/etc/run_clustalx
+++ b/etc/run_clustalx
@@ -36,6 +36,6 @@ perl -pne 'if (/^>(\S+)/) {
   }
 }' $temp_file_name > $temp_file_name.processed
 
-clustalx $temp_file_name.processed
+clustalx -INFILE=$temp_file_name.processed
 
 exit 0