diff --git a/mmseq-flags.patch b/mmseq-flags.patch
index b3c361c..6a8593d 100644
--- a/mmseq-flags.patch
+++ b/mmseq-flags.patch
@@ -1,5 +1,5 @@
---- mmseq_0.9.14/Makefile	2011-09-20 11:27:55.000000000 +0100
-+++ mmseq_0.9.14.new/Makefile	2011-10-07 16:13:01.261226334 +0100
+--- mmseq_0.9.14/src/Makefile	2011-09-20 11:27:55.000000000 +0100
++++ mmseq_0.9.14.new/src/Makefile	2011-10-07 16:13:01.261226334 +0100
 @@ -35,7 +35,7 @@
  	$(CXX) $(CXXFLAGS) -c sokal.cc
  
diff --git a/mmseq-sam-header.patch b/mmseq-sam-header.patch
index 5da50cb..a30dde0 100644
--- a/mmseq-sam-header.patch
+++ b/mmseq-sam-header.patch
@@ -1,5 +1,5 @@
---- mmseq_0.9.14/bam2hits.cpp	2011-09-22 16:24:55.000000000 +0100
-+++ mmseq_0.9.14.new/bam2hits.cpp	2011-10-07 15:22:12.387102321 +0100
+--- mmseq_0.9.14/src/bam2hits.cpp	2011-09-22 16:24:55.000000000 +0100
++++ mmseq_0.9.14.new/src/bam2hits.cpp	2011-10-07 15:22:12.387102321 +0100
 @@ -15,7 +15,7 @@
  **    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
  */