diff --git a/src/hhalignment.cpp b/src/hhalignment.cpp
index 88f5a05f..d95d967e 100755
--- a/src/hhalignment.cpp
+++ b/src/hhalignment.cpp
@@ -1673,11 +1673,20 @@ int Alignment::Filter2(char keep[], int coverage, int qid, float qsc,
   }
 
   // Sort sequences according to length; afterwards, nres[ksort[kk]] is sorted by size
+
+  struct sortDesc
+  {
+    int* _nres;
+    sortDesc(int* nres) : _nres(nres){}
+    bool operator()(int left, int right) {
+      return _nres[left] > _nres[right];
+    }
+  };
   if (ksort == NULL) {
     ksort = new int[N_in];  // never reuse alignment object for new alignment with more sequences
     for (k = 0; k < N_in; ++k)
       ksort[k] = k;
-    QSortInt(nres, ksort, kfirst + 1, N_in - 1, -1);  //Sort sequences after kfirst (query) in descending order
+    std::stable_sort(ksort + kfirst + 1 , ksort+ N_in, sortDesc(nres));  //Sort sequences after kfirst (query) in descending order
   }
   for (kk = 0; kk < N_in; ++kk) {
     inkk[kk] = in[ksort[kk]];