mdust/Makefile    |   18 +++++++++---------
 mdust/fastafile.c |    3 ++-
 mdust/mdust.c     |    1 +
 trimpoly/Makefile |   16 ++++++++--------
 4 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/mdust/Makefile b/mdust/Makefile
index 81bf4e9..0c75e69 100644
--- a/mdust/Makefile
+++ b/mdust/Makefile
@@ -1,40 +1,40 @@
 # Useful directories
 
 # Directories to search for header files
-SEARCHDIRS := -I. -I- 
+SEARCHDIRS := -I. -iquote
 
 
 #SYSTYPE :=     $(shell uname)
 
-CC      := gcc
-CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
+CC      ?= gcc
+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
 
 %.o : %.c
 	${CC} ${CFLAGS} -c $< -o $@
 
 %.o : %.cc
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 %.o : %.C
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 %.o : %.cpp
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 %.o : %.cxx
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 # C/C++ linker
 
 LINKER    := gcc
-LDFLAGS    =
 LOADLIBES := 
 
 .PHONY : all
 all:    mdust
 
 mdust:  ./mdust.o ./dust.o ./fastafile.o
-	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
 
 # target for removing all object files
 
diff --git a/mdust/fastafile.c b/mdust/fastafile.c
index 6c14b99..5f70f14 100644
--- a/mdust/fastafile.c
+++ b/mdust/fastafile.c
@@ -1,7 +1,8 @@
 #include <stdio.h>
 #include <ctype.h>
 #include <malloc.h>
-
+#include <string.h>
+#include <stdlib.h>
 #include "fastafile.h"
 
 
diff --git a/mdust/mdust.c b/mdust/mdust.c
index f2bae99..c3ee686 100644
--- a/mdust/mdust.c
+++ b/mdust/mdust.c
@@ -1,6 +1,7 @@
 #include <stdlib.h>
 #include <stdio.h>
 #include <ctype.h>
+#include <string.h>
 #include "dust.h"
 #include "fastafile.h"
 
diff --git a/trimpoly/Makefile b/trimpoly/Makefile
index 84db22d..71145c2 100644
--- a/trimpoly/Makefile
+++ b/trimpoly/Makefile
@@ -3,28 +3,28 @@
 # Directories to search for header files
 SEARCHDIRS := -I.
 
-CC      := gcc
-CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
+CC      ?= gcc
+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
 
 %.o : %.c
 	${CC} ${CFLAGS} -c $< -o $@
 
 %.o : %.cc
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 %.o : %.C
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 %.o : %.cpp
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 %.o : %.cxx
-	${CC} ${CFLAGS} -c $< -o $@
+	${CXX} ${CXXFLAGS} -c $< -o $@
 
 # C/C++ linker
 
 LINKER    := gcc
-LDFLAGS    = 
 LOADLIBES =
 SYSTYPE :=     $(shell uname)
 #ifeq ($(SYSTYPE), Linux)
@@ -37,7 +37,7 @@ SYSTYPE :=     $(shell uname)
 all:    trimpoly
 
 trimpoly:  ./trimpoly.o color_c.o
-	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
 
 # target for removing all object files