diff --git a/delstop.d b/delstop.d
index f0af3a0..8b18acc 100644
--- a/delstop.d
+++ b/delstop.d
@@ -139,27 +139,39 @@ void processFastaNT(string filePath, const FastaData fastaData) {
     std.file.write(filePath, lines.join("\n"));  
 }
 
-void processFasta(string fasta_aa, string fasta_nt){
+void processFasta(string fasta_aa, string fasta_nt, string enableDelete){
     // get pos from fasta_aa & modify
     FastaData fastaData = processFastaAA(fasta_aa);
 
     if (fastaData.foundSpecialChar) {
-        // if found special, proces fasta_nt
-        // backup fasta_aa
-        backup(fasta_nt);  // modify fasta_nt
+        backup(fasta_nt);  // backup fasta_nt
         processFastaNT(fasta_nt, fastaData);  // modify fasta_nt
+    }
+    if (enableDelete == "--delete"){ // delete the nt's gap to meet the requirement of trimal
+	if(!fastaData.foundSpecialChar){
+	    backup(fasta_nt);
+	}
+	string content = readText(fasta_nt);
+        content = replace(content, "-", "");
+        std.file.write(fasta_nt, content);
     } 
 }
 
 void main(string[] args) {
-    if (args.length < 3) {
-        writeln("Usage: program <fasta_aa> <fasta_nt>");
+    if (args.length != 3 && args.length != 4) {
+        writeln("\t\t\tDelete StopCondon generated by Macse\n\t\t\t\tAuthor: Guoyi Zhang\n\t\tUsage: " ~ args[0] ~ " <fasta_aa> <fasta_nt> --delete\n\t\tNote: fasta_aa and fasta_nt should be macse output files\n\t\t--delete should be used when downstream software is tirmal");
         return;
     }
-
+    
     string fasta_aa = args[1];
     string fasta_nt = args[2];
+    string enableDelete;
+    if(args.length>3){
+    	enableDelete = args[3];
+    } else {
+	enableDelete = "";
+    }
 
-    processFasta(fasta_aa, fasta_nt);
+    processFasta(fasta_aa, fasta_nt, enableDelete);
 }