Index: src/jalview/ws/slivkaws/SlivkaWSInstance.java
===================================================================
diff -u -N -rc8dfa0a1b91d46b9c11dc6ce7b2b4bfcbc71c13e -r65c32aa39e51d66319b48f0783ef152b07cd5d8e
--- src/jalview/ws/slivkaws/SlivkaWSInstance.java	(.../SlivkaWSInstance.java)	(revision c8dfa0a1b91d46b9c11dc6ce7b2b4bfcbc71c13e)
+++ src/jalview/ws/slivkaws/SlivkaWSInstance.java	(.../SlivkaWSInstance.java)	(revision 65c32aa39e51d66319b48f0783ef152b07cd5d8e)
@@ -95,8 +95,11 @@
           format = FileFormat.Fasta;
           break;
         }
-        InputStream stream = new ByteArrayInputStream(
-            fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
+        
+        // we avoid any use of Jalview's user facing export routines here
+        
+        InputStream stream = new ByteArrayInputStream(format.getWriter(null)
+                .print(sequences.toArray(new SequenceI[0]), false)
                 .getBytes());
         request.addFile(param.getId(), stream);
       }