Makefile minor tweaks

Makefile

@@ -14,18 +14,20 @@ CamlPaml:
 	cd lib/CamlPaml; $(MAKE) $(MFLAGS) reinstall
 
 cde-package: PhyloCSF CDE
+	rm -rf cde-package cde-package.$(ARCH)
 	CDE/cde ./PhyloCSF.$(ARCH) 12flies PhyloCSF_Examples/tal-AA.fa 
-	CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/ALDH2.exon5.fa --frames=3
-	#CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/Aldh2.mRNA.fa --frames=3 --removeRefGaps --aa
+	CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/ALDH2.exon5.fa --frames=3 --allScores
+	CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/Aldh2.mRNA.fa --strategy=fixed --frames=3 --orf=ATGStop --minCodons=400 --allScores --removeRefGaps --aa
 	mv cde-package cde-package.$(ARCH)
 	tar -cf cde-package.$(ARCH).tar cde-package.$(ARCH)
 
 CDE:
-	cd CDE && make
+	git submodule update --init
+	cd CDE && $(MAKE)
 
 clean:
 	cd lib/CamlPaml; $(MAKE) clean
 	cd src; $(MAKE) clean
 	rm -f PhyloCSF.*
 	rm -rf cde-package*
-	cd CDE && make clean || true
+	cd CDE && $(MAKE) clean || true