diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..1933786
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+/test/
diff --git a/src/Makefile b/src/Makefile
index 756328f..9bb5afb 100755
--- a/src/Makefile
+++ b/src/Makefile
@@ -30,7 +30,8 @@ DIRS = aragorn   \
        sumaclust \
        sumatra   \
        gawk      \
-       getopt
+       getopt    \
+       cd-hit
 
 include ../config/targets/propagate.targ
 
diff --git a/src/cd-hit/Makefile b/src/cd-hit/Makefile
new file mode 100644
index 0000000..135ce42
--- /dev/null
+++ b/src/cd-hit/Makefile
@@ -0,0 +1,26 @@
+# ---------------------------------------------------------------
+# $Id: $
+# ---------------------------------------------------------------
+# @file: Makefile
+# @desc: makefile for package exonerate
+#
+# @history:
+# @+	    <Gloup> : Sept 15 : Adapted to ORG.Annot
+#
+# @note: should be processed with gnu compatible make
+# @note: helixware_compatible
+#
+# @end:
+# ---------------------------------------------------------------
+#
+
+include ../../config/auto.conf
+
+PKG = cd-hit-v4.6.4-2015-0603
+
+MAKEOPTIONS= openmp=no PREFIX=$(PRTPATH)/bin
+
+include $(CFGDIR)targets/package.targ
+
+include $(CFGDIR)targets/help.targ
+
diff --git a/src/cd-hit/cd-hit-v4.6.4-2015-0603.tgz b/src/cd-hit/cd-hit-v4.6.4-2015-0603.tgz
new file mode 100644
index 0000000..63cc0a0
Binary files /dev/null and b/src/cd-hit/cd-hit-v4.6.4-2015-0603.tgz differ
diff --git a/src/muscle/muscle3.8.31/muscle.make.stderr.txt b/src/muscle/muscle3.8.31/muscle.make.stderr.txt
index e69de29..9780f46 100644
--- a/src/muscle/muscle3.8.31/muscle.make.stderr.txt
+++ b/src/muscle/muscle3.8.31/muscle.make.stderr.txt
@@ -0,0 +1,60 @@
+alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
+        switch (Alpha)
+                ^
+1 warning generated.
+clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
+        switch (m_JoinStyle)
+                ^
+clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
+        switch (m_CentroidStyle)
+                ^
+clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
+        switch (m_JoinStyle)
+                ^
+3 warnings generated.
+glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch]
+        switch (g_PPScore)
+                ^
+1 warning generated.
+msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
+        switch (Method)
+                ^
+1 warning generated.
+objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch]
+        switch (OS)
+                ^
+1 warning generated.
+objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
+        switch (g_TermGaps)
+                ^
+1 warning generated.
+params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
+        switch (g_PPScore)
+                ^
+1 warning generated.
+In file included from profdb.cpp:9:
+In file included from ./clustsetmsa.h:8:
+./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
+                switch(m_Distance)
+                       ^
+1 warning generated.
+profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
+        switch (g_Alpha)
+                ^
+1 warning generated.
+In file included from refine.cpp:9:
+In file included from ./clustsetmsa.h:8:
+./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
+                switch(m_Distance)
+                       ^
+1 warning generated.
+subfams.cpp:44:25: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
+        for (unsigned i = 0; i < uNodeCount; ++i)
+                             ~ ^ ~~~~~~~~~~
+1 warning generated.
+In file included from treefrommsa.cpp:5:
+In file included from ./clustsetmsa.h:8:
+./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]
+                switch(m_Distance)
+                       ^
+1 warning generated.