diff --git a/src/main.mk b/src/main.mk
index 3e8c41ffc..c1117bd73 100644
--- a/src/main.mk
+++ b/src/main.mk
@@ -32,10 +32,6 @@ SOURCES      := AS_global.C \
                 \
                 utility/AS_UTL_alloc.C \
                 \
-                utility/bitEncodings.C \
-                utility/bitPackedFile.C \
-                utility/bitPackedArray.C \
-                utility/dnaAlphabets.C \
                 utility/hexDump.C \
                 utility/md5.C \
                 utility/memoryMappedFile.C \
@@ -45,7 +41,6 @@ SOURCES      := AS_global.C \
                 utility/speedCounter.C \
                 utility/sweatShop.C \
                 utility/timeAndSize.C \
-                utility/kMer.C \
                 \
                 correction/computeGlobalScore.C \
                 correction/falconConsensus.C \
@@ -74,8 +69,6 @@ SOURCES      := AS_global.C \
                 stores/libsnappy/snappy-stubs-internal.cc \
                 stores/libsnappy/snappy.cc \
                 \
-                meryl-san/libmeryl-san.C \
-                \
                 overlapInCore/overlapReadCache.C \
                 \
                 overlapErrorAdjustment/analyzeAlignment.C \
@@ -115,17 +108,6 @@ SOURCES      := AS_global.C \
                 gfa/gfa.C \
                 gfa/bed.C \
                 \
-                meryl-san/libkmer/existDB-create-from-fasta.C \
-                meryl-san/libkmer/existDB-create-from-meryl.C \
-                meryl-san/libkmer/existDB-create-from-sequence.C \
-                meryl-san/libkmer/existDB-state.C \
-                meryl-san/libkmer/existDB.C \
-                meryl-san/libkmer/positionDB-access.C \
-                meryl-san/libkmer/positionDB-dump.C \
-                meryl-san/libkmer/positionDB-file.C \
-                meryl-san/libkmer/positionDB-mismatch.C \
-                meryl-san/libkmer/positionDB-sort.C \
-                meryl-san/libkmer/positionDB.C
 
 
 
@@ -157,7 +139,6 @@ SRC_INCDIRS  := . \
                 utgcns/libpbutgcns \
                 utgcns/libNDFalcon \
                 utgcns/libboost \
-                meryl-san/libleaff \
                 overlapInCore \
                 overlapInCore/libedlib \
                 overlapInCore/liboverlap
@@ -194,7 +175,6 @@ SUBMAKEFILES := stores/dumpBlob.mk \
                 meryl-san/positionDB.mk \
                 meryl-san/simple-dump.mk \
                 \
-                merTrim/merTrim.mk \
                 \
                 overlapInCore/overlapInCore.mk \
                 overlapInCore/overlapInCorePartition.mk \
diff --git a/src/meryl-san/estimate-mer-threshold.mk b/src/meryl-san/estimate-mer-threshold.mk
index 53207220f..45c3afc55 100644
--- a/src/meryl-san/estimate-mer-threshold.mk
+++ b/src/meryl-san/estimate-mer-threshold.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := estimate-mer-threshold
 SOURCES  := estimate-mer-threshold.C
 
-SRC_INCDIRS := .. ../utility libleaff
+SRC_INCDIRS := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/meryl-san/existDB.mk b/src/meryl-san/existDB.mk
index 121ceb3b8..291d37881 100644
--- a/src/meryl-san/existDB.mk
+++ b/src/meryl-san/existDB.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := existDB
 SOURCES  := existDB.C
 
-SRC_INCDIRS  := .. ../utility libleaff libkmer
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/meryl-san/leaff.mk b/src/meryl-san/leaff.mk
index d9dc971c2..7d7e6c55c 100644
--- a/src/meryl-san/leaff.mk
+++ b/src/meryl-san/leaff.mk
@@ -17,7 +17,7 @@ SOURCES  := leaff-blocks.C \
             leaff-statistics.C \
             leaff.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/meryl-san/libleaff.mk b/src/meryl-san/libleaff.mk
index 34dc165d2..c1ac68c60 100644
--- a/src/meryl-san/libleaff.mk
+++ b/src/meryl-san/libleaff.mk
@@ -9,7 +9,8 @@ ifeq "$(strip ${TARGET_DIR})" ""
 endif
 
 TARGET   := libleaff.a
-SOURCES  := libleaff/fastaFile.C \
+SOURCES  := libleaff/dnaAlphabets.C \
+            libleaff/fastaFile.C \
             libleaff/fastaStdin.C \
             libleaff/fastqFile.C \
             libleaff/fastqStdin.C \
@@ -19,14 +20,30 @@ SOURCES  := libleaff/fastaFile.C \
             libleaff/seqFactory.C \
             libleaff/seqStore.C \
             libleaff/seqStream.C \
-            libleaff/sffFile.C
+            libleaff/sffFile.C \
+            utility/bitEncodings.C \
+            utility/bitPackedFile.C \
+            utility/bitPackedArray.C \
+            utility/kMer.C \
+            libkmer/existDB-create-from-fasta.C \
+            libkmer/existDB-create-from-meryl.C \
+            libkmer/existDB-create-from-sequence.C \
+            libkmer/existDB-state.C \
+            libkmer/existDB.C \
+            libkmer/positionDB-access.C \
+            libkmer/positionDB-dump.C \
+            libkmer/positionDB-file.C \
+            libkmer/positionDB-mismatch.C \
+            libkmer/positionDB-sort.C \
+            libkmer/positionDB.C \
+            libmeryl-san.C
 
 #            libleaff/selftest.C
 #            libleaff/test-merStream.C
 #            libleaff/test-seqCache.C
 #            libleaff/test-seqStream.C
 
-SRC_INCDIRS  := .. ../utility ../stores
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := 
diff --git a/src/utility/dnaAlphabets.C b/src/meryl-san/libleaff/dnaAlphabets.C
similarity index 100%
rename from src/utility/dnaAlphabets.C
rename to src/meryl-san/libleaff/dnaAlphabets.C
diff --git a/src/utility/dnaAlphabets.H b/src/meryl-san/libleaff/dnaAlphabets.H
similarity index 100%
rename from src/utility/dnaAlphabets.H
rename to src/meryl-san/libleaff/dnaAlphabets.H
diff --git a/src/meryl-san/maskMers.mk b/src/meryl-san/maskMers.mk
index 015439b0d..20a98f498 100644
--- a/src/meryl-san/maskMers.mk
+++ b/src/meryl-san/maskMers.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := maskMers
 SOURCES  := maskMers.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/meryl-san/meryl-san.mk b/src/meryl-san/meryl-san.mk
index 60f8412db..6f29cdb81 100644
--- a/src/meryl-san/meryl-san.mk
+++ b/src/meryl-san/meryl-san.mk
@@ -18,7 +18,7 @@ SOURCES  := meryl-args.C \
             meryl-unaryOp.C \
             meryl-san.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/meryl-san/positionDB.mk b/src/meryl-san/positionDB.mk
index e2ba60719..27975ffa8 100644
--- a/src/meryl-san/positionDB.mk
+++ b/src/meryl-san/positionDB.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := positionDB
 SOURCES  := positionDB.C
 
-SRC_INCDIRS  := .. ../utility libleaff libkmer
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/meryl-san/simple-dump.mk b/src/meryl-san/simple-dump.mk
index 130176c0e..e6c72b7a4 100644
--- a/src/meryl-san/simple-dump.mk
+++ b/src/meryl-san/simple-dump.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := simple-dump
 SOURCES  := simple-dump.C
 
-SRC_INCDIRS  := .. ../utility libleaff libkmer
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer  .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/meryl-san/simple.mk b/src/meryl-san/simple.mk
index 6e08a410c..d04cb980b 100644
--- a/src/meryl-san/simple.mk
+++ b/src/meryl-san/simple.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := simple
 SOURCES  := simple.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu
diff --git a/src/utility/bitEncodings.C b/src/meryl-san/utility/bitEncodings.C
similarity index 100%
rename from src/utility/bitEncodings.C
rename to src/meryl-san/utility/bitEncodings.C
diff --git a/src/utility/bitEncodings.H b/src/meryl-san/utility/bitEncodings.H
similarity index 100%
rename from src/utility/bitEncodings.H
rename to src/meryl-san/utility/bitEncodings.H
diff --git a/src/utility/bitOperations.H b/src/meryl-san/utility/bitOperations.H
similarity index 100%
rename from src/utility/bitOperations.H
rename to src/meryl-san/utility/bitOperations.H
diff --git a/src/utility/bitPackedArray.C b/src/meryl-san/utility/bitPackedArray.C
similarity index 100%
rename from src/utility/bitPackedArray.C
rename to src/meryl-san/utility/bitPackedArray.C
diff --git a/src/utility/bitPackedArray.H b/src/meryl-san/utility/bitPackedArray.H
similarity index 100%
rename from src/utility/bitPackedArray.H
rename to src/meryl-san/utility/bitPackedArray.H
diff --git a/src/utility/bitPackedFile.C b/src/meryl-san/utility/bitPackedFile.C
similarity index 100%
rename from src/utility/bitPackedFile.C
rename to src/meryl-san/utility/bitPackedFile.C
diff --git a/src/utility/bitPackedFile.H b/src/meryl-san/utility/bitPackedFile.H
similarity index 100%
rename from src/utility/bitPackedFile.H
rename to src/meryl-san/utility/bitPackedFile.H
diff --git a/src/utility/bitPacking.H b/src/meryl-san/utility/bitPacking.H
similarity index 100%
rename from src/utility/bitPacking.H
rename to src/meryl-san/utility/bitPacking.H
diff --git a/src/utility/kMer.C b/src/meryl-san/utility/kMer.C
similarity index 100%
rename from src/utility/kMer.C
rename to src/meryl-san/utility/kMer.C
diff --git a/src/utility/kMer.H b/src/meryl-san/utility/kMer.H
similarity index 100%
rename from src/utility/kMer.H
rename to src/meryl-san/utility/kMer.H
diff --git a/src/utility/kMerHuge.H b/src/meryl-san/utility/kMerHuge.H
similarity index 100%
rename from src/utility/kMerHuge.H
rename to src/meryl-san/utility/kMerHuge.H
diff --git a/src/utility/kMerTiny.H b/src/meryl-san/utility/kMerTiny.H
similarity index 100%
rename from src/utility/kMerTiny.H
rename to src/meryl-san/utility/kMerTiny.H