--- a/src/Makefile
+++ b/src/Makefile
@@ -4,7 +4,7 @@
 include ../common.mk
 CC	= g++
 
-# Notes: - "-Wno-sign-compare" eliminates a high number of warnings (see footnote below). Please adopt 
+# Notes: - "-Wno-sign-compare" eliminates a high number of warnings (see footnote below). Please adopt
 #          a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
 #        - The order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
 CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -g -ggdb -O3 ${CFLAGS} # -DDEBUG -DDEBUG_STATES
@@ -37,14 +37,14 @@
 	INCLS += -I/usr/include/lpsolve
 endif
 DUMOBJS = dummy.o
-TOBJS	= commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # contentmodel.o baumwelch.o 
+TOBJS	= commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # contentmodel.o baumwelch.o
 PROGR	= augustus etraining consensusFinder curve2hints prepareAlign fastBlockSearch
 INFO    = cflags
 
 ifdef MYSQL
 # replace RUNTIME_LIBPATH with your own run-time libpath if mysql++ is not installed system-wide, e.g.
-# RUNTIME_LIBPATH = -Wl,-rpath=/home/mario/augustus/trunks/mysql++/mysql++-3.1.0/lib 
-RUNTIME_LIBPATH = 
+# RUNTIME_LIBPATH = -Wl,-rpath=/home/mario/augustus/trunks/mysql++/mysql++-3.1.0/lib
+RUNTIME_LIBPATH =
 INCLS	+= -I/usr/include/mysql -I/usr/include/mysql++ # the path to mysql++ may have to be adjusted
 LIBS 	+=  -lmysqlclient -lmysqlpp ${RUNTIME_LIBPATH} # -L/usr/local/lib/libmysqlpp.so.3.1.0
 CFLAGS  += -DAMYSQL
@@ -70,18 +70,18 @@
 	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp augustus ../bin/
 
-etraining: etraining.cc $(TOBJS) $(OBJS) 
+etraining: etraining.cc $(TOBJS) $(OBJS)
 	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp etraining ../bin/
 
 evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
 	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 
-consensusFinder: consensusFinder.cc consensus.o 
+consensusFinder: consensusFinder.cc consensus.o
 	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp consensusFinder ../bin/
 
-curve2hints: curve2hints.cc exon_seg.o 
+curve2hints: curve2hints.cc exon_seg.o
 	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp curve2hints ../bin/
 
@@ -110,7 +110,7 @@
 	echo "$(CFLAGS)" > $(INFO)
 
 clean:
-	rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o  $(INFO) 
+	rm -f ../bin/* $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o  $(INFO)
 
 tidy: clean
 	rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)
