sources/makefile |   15 +++++--------
 train/makefile   |   59 +++++++++++++++++++++++++++++++----------------------
 2 files changed, 40 insertions(+), 34 deletions(-)

diff --git a/sources/makefile b/sources/makefile
index f287d71..c560f48 100644
--- a/sources/makefile
+++ b/sources/makefile
@@ -2,25 +2,22 @@
 
 
 
-CC=g++
-CFLAGS=-g
-
 all: glimmerhmm
 
 glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
-	$(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
 
 glimmerhmm.o: glimmerhmm.c
-	$(CC) $(CFLAGS) -c glimmerhmm.c
+	$(CXX) $(CXXFLAGS) -c glimmerhmm.c
 
 graph.o: graph.c 
-	$(CC) $(CFLAGS) -c graph.c
+	$(CXX) $(CXXFLAGS) -c graph.c
 
 sites.o: sites.c
-	$(CC) $(CFLAGS) -c sites.c
+	$(CXX) $(CXXFLAGS) -c sites.c
 
 tree_util_prob.o: tree_util_prob.c
-	$(CC) $(CFLAGS) -c tree_util_prob.c
+	$(CXX) $(CXXFLAGS) -c tree_util_prob.c
 
 util.o: util.c
-	$(CC) $(CFLAGS) -c util.c
+	$(CXX) $(CXXFLAGS) -c util.c
diff --git a/train/makefile b/train/makefile
index 2383f18..d5a7107 100644
--- a/train/makefile
+++ b/train/makefile
@@ -2,9 +2,6 @@
 
 # C compiler
 
-C       = gcc 
-CC      = g++ 
-CFLAGS  = -O1 ${SEARCHDIRS}
 #CFLAGS  = -O3 -g -Wall
 LIBS    = -lm
 
@@ -15,64 +12,76 @@ all:    build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
 
 
 misc.o: misc.c
-	${C} ${CFLAGS} -c misc.c
+	$(CC) $(CFLAGS) -c misc.c
 
 build-icm.o: build-icm.c
-	${C} ${CFLAGS} -c build-icm.c
+	$(CC) $(CFLAGS) -c build-icm.c
 
 build-icm: build-icm.o misc.o
-	$(C) -o $@ build-icm.o misc.o $(LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
 
 build-icm-noframe.o: build-icm-noframe.c
-	${C} ${CFLAGS} -c build-icm-noframe.c
+	$(CC) $(CFLAGS) -c build-icm-noframe.c
 
 build-icm-noframe: build-icm-noframe.o misc.o
-	$(C) -o $@ build-icm-noframe.o misc.o $(LIBS)
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
 
 build1: build1.o
-	${CC} build1.c -o build1 $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS)
 
 build2: build2.o
-	${CC} build2.c -o build2 $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS)
 
 falsecomp: falsecomp.o
-	${CC} falsecomp.c -o falsecomp $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS)
 
 findsites: findsites.o
-	${CC} findsites.c -o findsites $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS)
 
 karlin: karlin.o
-	${CC} karlin.c -o karlin $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS)
 
 score: score.o
-	${CC} score.c -o score $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS)
 
 score2: score2.o
-	${CC} score2.c -o score2 $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS)
 
 scoreATG: scoreATG.o
-	${CC} scoreATG.c -o scoreATG $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS)
 
 scoreATG2: scoreATG2.o
-	${CC} scoreATG2.c -o scoreATG2 $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS)
 
 scoreSTOP: scoreSTOP.o
-	${CC} scoreSTOP.c -o scoreSTOP $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS)
 
 escoreSTOP2: scoreSTOP2.o
-	${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS)
 
-rfapp: erfapp.o
-	${CC} erfapp.c -o erfapp $(LIBS)
+erfapp: erfapp.o
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
 
 sites.o: sites.c
-	${CC} ${CFLAGS} -c sites.c
+	$(CXX) $(CXXFLAGS) -c sites.c
+
+scoreATG.o: scoreATG.c
+	$(CXX) $(CXXFLAGS) -c scoreATG.c
+	
+scoreSTOP.o: scoreSTOP.c
+	$(CXX) $(CXXFLAGS) -c scoreSTOP.c
+
+scoreSTOP2.o: scoreSTOP2.c
+	$(CXX) $(CXXFLAGS) -c scoreSTOP2.c
+
+scoreATG2.o: scoreATG2.c
+	$(CXX) $(CXXFLAGS) -c scoreATG2.c
 
 utils.o: utils.c 
-	${CC} ${CFLAGS} -c utils.c
+	$(CXX) $(CXXFLAGS) -c utils.c
 
 splicescore.o: splicescore.c
-	${CC} ${CFLAGS} -c splicescore.c
+	$(CXX) $(CXXFLAGS) -c splicescore.c
 
 splicescore: splicescore.o sites.o utils.o
-	${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)