[med-svn] [Git][med-team/fastml][upstream] New upstream version 3.11

Andreas Tille gitlab at salsa.debian.org
Sat Jul 27 20:35:30 BST 2019 


Andreas Tille pushed to branch upstream at Debian Med / fastml


Commits:
05b00510 by Andreas Tille at 2019-07-19T18:15:39Z
New upstream version 3.11
- - - - -


10 changed files:

- + libs/phylogeny/#Makefile#
- libs/phylogeny/Makefile
- libs/phylogeny/errorMsg.cpp
- + libs/phylogeny/make.dep
- libs/phylogeny/someUtil.cpp
- programs/Makefile.generic
- programs/fastml/bbReport.cpp
- + programs/fastml/make.dep
- + programs/gainLoss/make.dep
- + programs/indelCoder/make.dep


Changes:

=====================================
libs/phylogeny/#Makefile#
=====================================
@@ -0,0 +1,238 @@
+#! /usr/local/bin/gmake
+# $Id: Makefile 11759 2013-09-24 13:45:40Z elilevy $
+# makfile for yaep5
+
+
+
+# use LOGREP=t or DOUBLEREP=t to activate logRep or doubleRep respectively (or setenv DOUBLEREP in the shell)
+#DOUBLEREP=t
+#LOGREP=t
+
+
+Libsources= AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp				\
+   allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp			\
+   bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp			\
+   bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp	\
+   chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp			\
+   computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp				\
+   computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp			\
+   computeSubstitutionCounts.cpp											\
+   computePosteriorExpectationOfSubstitutions.cpp							\
+   computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp			\
+   ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp	\
+   distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp				\
+   fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp					\
+   fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp 	\
+   fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp				\
+   generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp	\
+   generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp		\
+   granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp \
+   likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp						\
+   likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp				\
+   molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp				\
+   nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp			\
+   pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp		\
+   replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp			\
+   sequence.cpp sequenceContainer.cpp simulateTree.cpp					\
+   siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp				\
+   splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp			\
+   talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp			\
+   uniformDistribution.cpp cmdline2EvolObjs.cpp						\
+   generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp					\
+   givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp					\
+   posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp			\
+   logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp					\
+   replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp		\
+   C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp			\
+   betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp				\
+   samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp				\
+   likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp			\
+   fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp				\
+   tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp			\
+   simulateCodonsJumps.cpp													\
+   simulateJumpsAbstract.cpp												\
+   ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp\
+   extremeValDistribution.cpp \
+   gammaDistributionFixedCategories.cpp  generalGammaDistributionPlusInvariant.cpp  gammaDistributionPlusInvariant.cpp   \
+   distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp 					\
+   optGammaMixtureLS.cpp mixtureDistribution.cpp  suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp \
+   wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp	\
+	threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp	\
+	bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp\
+	gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp
+
+# do not use: fromInstructionFile.cpp, simulateSequnce.cpp  split.save.cpp
+
+
+# LibCsources= cmdline.c
+# LibCsources += getopt.c getopt1.c 
+
+EXEC = 
+#TEST_EXEC_SUB = split_test splitMap_test bootstrap_test
+TEST_EXEC = $(addprefix tests/,$(TEST_EXEC_SUB))
+LIB = libEvolTree.a
+DEBUGLIB = $(LIB:.a=Debug.a)
+DOUBLEREPLIB = $(LIB:.a=DoubleRep.a)
+
+
+#CC=g++
+CXX=g++
+CC=$(CXX)
+
+#requres 2.13, but may work with 2.11
+GENGETOPT = gengetopt
+# osX/tiger
+#GENGETOPT = /opt/local/bin/gengetopt
+
+.SECONDARY: semphy_cmdline.c semphy_cmdline.h
+
+#LDFLAGS=  
+
+CPPFLAGS=  -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32AGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -DVERBOS
+#CPPFLAGSDOU=  $(CPPFLAGS) 
+#-pg
+
+
+#CPPFLAGS+= -I/usr/include/g++-v3
+#CPPFLAGS+= -DLOG -DLOGCLS -DMEMCHK
+
+# sources
+sources= $(Libsources) $(LibCsources) $(addsuffix .cpp,$(EXEC) $(TEST_EXEC))
+
+.PHONY: tests lib test debug %.debug
+.PHONY:  dat DOUBLEREP doubleRep
+
+all: lib $(EXEC)
+
+test: all tests
+	+cd tests; make -k test
+
+#ifdef DOUBLEREP
+#CPPFLAGS+= -DLOGREP
+#CPPFLAGSDEBUG += -DLOGREP
+#LDFLAGSDEBUG +=  -DLOGREP
+#endif
+
+ifdef DOUBLEREP
+CPPFLAGS+= -DDOUBLEREP
+CPPFLAGSDEBUG += -DDOUBLEREP
+LDFLAGSDEBUG +=  -DDOUBLEREP
+endif
+
+debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32
+debug:  $(DEBUGLIB)
+pl:
+	@echo "lib  ="$(LIB)
+	@echo "debug="$(DEBUGLIB)
+#debug: all 
+#	cp libEvolTree.a libEvolTreeDebug.a
+
+# <<<<<<< Makefile
+# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25
+# % debug: LIB = libEvolTreeDebug.a
+# %.debug: %
+# 	@echo "made \""$(*)"\" in debug mode"
+
+# =======
+#>>>>>>> 2.34
+
+lib: $(LIB)
+
+$(LIB): $(Libsources:.cpp=.o) $(LibCsources:.c=.o)
+	ar rv $@ $?
+	ranlib $@
+
+tags: *.cpp *.h
+	etags --members --language=c++ $^ 
+
+$(EXEC) $(TEST_EXEC): $(LIB)
+tests: $(TEST_EXEC)
+
+-include make.dep
+
+install:
+	cd ../fast; make -f Makefile.lib install_do
+
+
+clean:
+	-rm -f $(LIB) $(DEBUGLIB) $(DOUBLEREPLIB) $(EXEC) $(TEST_EXEC) *.o
+
+
+ifneq ($(wildcard make.dep), make.dep)
+ make.dep: depend
+endif
+
+depend makedep: _make.dep
+	@mv -f _make.dep make.dep 
+
+_make.dep: $(sources)
+	@echo making depend
+#	$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@ ; [ -s $@ ] || rm -f $@' 
+	@$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed "s/\(^[^.]*\)\.o/\1.o \1.debug.o/g" > $@' 
+_fast:
+	cd ../fast;make -f Makefile.lib -k all
+
+fast.% _fast.%:
+	cd ../fast;make -f Makefile.lib -k $(*)
+
+
+simulateSequnce: simulateSequnce_cmdline.o
+
+
+evolObjsTest.ggo: evolObjs.header evolObjs.args
+	cat $^ > $@
+
+
+# commandline (gengetopts)
+%_cmdline.h %_cmdline.c: %.ggo
+	$(GENGETOPT)  -i$< -F$(*)_cmdline
+
+%.dat.q: %.dat
+	awk 'BEGIN{RS="[\n\r]+";};{print "\" "$$0" \"\r"}' $< >  $@
+#	cat $@
+
+DAT = cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q
+
+dat: $(DAT)
+
+cleandat:
+	rm $(DAT)
+
+datMatrixHolder.o: $(DAT)
+
+.PRECIOUS: $(DAT)
+
+debug: LIB = $(DEBUGLIB)
+
+%.debug: CPPFLAGS = $(CPPFLAGSDEBUG)
+%.debug: %
+	@echo "made \""$(*)"\" in debug mode"
+
+
+%.debug.o: %.c
+	$(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@
+
+%.debug.o: %.cpp
+	$(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@
+
+$(DEBUGLIB): $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o)
+	ar rv $@ $?
+	ranlib $@
+
+#doubleRep: LOGREP=t
+#doubleRep: CPPFLAGS+= -DLOGREP
+doubleRep: DOUBLEREP=t
+doubleRep: CPPFLAGS+= -DDOUBLEREP
+doubleRep: $(DOUBLEREPLIB)
+
+%.doubleRep.o: %.c
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
+
+%.doubleRep.o: %.cpp
+	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
+
+$(DOUBLEREPLIB): $(Libsources:.cpp=.doubleRep.o) $(LibCsources:.c=.doubleRep.o)
+	ar rv $@ $?
+	ranlib $@
+
+# DO NOT DELETE


=====================================
libs/phylogeny/Makefile
=====================================
@@ -88,8 +88,8 @@ GENGETOPT = gengetopt
 
 #LDFLAGS=  
 
-CPPFLAGS=  -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32
-CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -DVERBOS
+CPPFLAGS=  -O3 -Wall -Wno-sign-compare -I. -DLOG 
+CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -DVERBOS
 #CPPFLAGSDOU=  $(CPPFLAGS) 
 #-pg
 
@@ -120,7 +120,7 @@ CPPFLAGSDEBUG += -DDOUBLEREP
 LDFLAGSDEBUG +=  -DDOUBLEREP
 endif
 
-debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32
+debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG 
 debug:  $(DEBUGLIB)
 pl:
 	@echo "lib  ="$(LIB)
@@ -129,7 +129,7 @@ pl:
 #	cp libEvolTree.a libEvolTreeDebug.a
 
 # <<<<<<< Makefile
-# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25
+# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG 
 # % debug: LIB = libEvolTreeDebug.a
 # %.debug: %
 # 	@echo "made \""$(*)"\" in debug mode"


=====================================
libs/phylogeny/errorMsg.cpp
=====================================
@@ -1,4 +1,4 @@
-// $Id: errorMsg.cpp 6066 2009-04-14 19:11:10Z itaymay $
+// $Id: errorMsg.cpp 15479 2016-10-10 16:25:21Z elilevy $
 
 // version 1.01
 // last modified 1 Jan 2004
@@ -16,7 +16,7 @@ void errorMsg::reportError(const vector<string>& textToPrint, const int exitCode
 	for (int i =0 ; i < textToPrint.size() ; ++i) {
 		LOG(1,<<textToPrint[i]<<endl);
 		cerr<<textToPrint[i]<<endl;
-		if (_errorOut != NULL && *_errorOut != cerr)  {
+		if (_errorOut != NULL && _errorOut != &cerr)  {
 			(*_errorOut)<<textToPrint[i]<<endl;
 		}
 	}
@@ -31,7 +31,7 @@ void errorMsg::reportError(const vector<string>& textToPrint, const int exitCode
 void errorMsg::reportError(const string& textToPrint, const int exitCode) {
 	LOG(1,<<endl<<textToPrint<<endl);
 	cerr<<endl<<textToPrint<<endl;
-	if (_errorOut != NULL && *_errorOut != cerr)  {
+	if (_errorOut != NULL && _errorOut != &cerr)  {
 		(*_errorOut)<<textToPrint<<endl;
 	}
 	if (errno!=0){


=====================================
libs/phylogeny/make.dep
=====================================
@@ -0,0 +1,820 @@
+AddLog.o AddLog.debug.o: AddLog.cpp AddLog.h
+NNiProp.o NNiProp.debug.o: NNiProp.cpp definitions.h treeIt.h errorMsg.h tree.h \
+ readTree.h logFile.h treeUtil.h NNiProp.h sequenceContainer.h sequence.h \
+ alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ bblEM.h countTableComponent.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h suffStatComponent.h unObservableData.h \
+ bblEMProportional.h
+NNiSep.o NNiSep.debug.o: NNiSep.cpp definitions.h treeIt.h errorMsg.h tree.h readTree.h \
+ logFile.h treeUtil.h NNiSep.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h bblEM.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ unObservableData.h bblEMSeperate.h
+Nni.o Nni.debug.o: Nni.cpp definitions.h treeUtil.h tree.h readTree.h errorMsg.h \
+ logFile.h treeIt.h Nni.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h bblEM.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ unObservableData.h
+aaJC.o aaJC.debug.o: aaJC.cpp aaJC.h replacementModel.h definitions.h errorMsg.h
+allTrees.o allTrees.debug.o: allTrees.cpp definitions.h allTrees.h tree.h readTree.h \
+ errorMsg.h logFile.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h treeUtil.h treeIt.h \
+ bblEM.h countTableComponent.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h suffStatComponent.h unObservableData.h
+allTreesSeparateModel.o allTreesSeparateModel.debug.o: allTreesSeparateModel.cpp definitions.h treeIt.h \
+ errorMsg.h tree.h readTree.h logFile.h allTreesSeparateModel.h \
+ sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \
+ gainLossAlphabet.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h bblEMSeperate.h
+alphabet.o alphabet.debug.o: alphabet.cpp alphabet.h
+amino.o amino.debug.o: amino.cpp amino.h definitions.h errorMsg.h alphabet.h \
+ geneticCodeHolder.h codon.h someUtil.h logFile.h
+bestAlpha.o bestAlpha.debug.o: bestAlpha.cpp bestAlpha.h definitions.h \
+ likelihoodComputation.h computePijComponent.h tree.h readTree.h \
+ errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h unObservableData.h bblEM.h countTableComponent.h \
+ bblEMProportionalEB.h bblLSProportionalEB.h numRec.h \
+ uniformDistribution.h
+bestAlphaManyTrees.o bestAlphaManyTrees.debug.o: bestAlphaManyTrees.cpp bestAlphaManyTrees.h \
+ definitions.h computePijComponent.h tree.h readTree.h errorMsg.h \
+ logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h bblEM.h \
+ countTableComponent.h suffStatComponent.h unObservableData.h \
+ likelihoodComputation.h bestAlpha.h numRec.h uniformDistribution.h \
+ bblEMProportional.h bblEMSeperate.h
+bestHKYparam.o bestHKYparam.debug.o: bestHKYparam.cpp bestHKYparam.h definitions.h \
+ likelihoodComputation.h computePijComponent.h tree.h readTree.h \
+ errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h unObservableData.h hky.h bblEM.h \
+ countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \
+ numRec.h uniformDistribution.h bestAlpha.h
+bootstrap.o bootstrap.debug.o: bootstrap.cpp definitions.h someUtil.h logFile.h alphabet.h \
+ bootstrap.h split.h splitMap.h tree.h readTree.h errorMsg.h treeUtil.h \
+ splitTreeUtil.h
+bblEM.o bblEM.debug.o: bblEM.cpp bblEM.h definitions.h tree.h readTree.h errorMsg.h \
+ logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h \
+ someUtil.h gainLossAlphabet.h countTableComponent.h \
+ computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h suffStatComponent.h unObservableData.h \
+ likelihoodComputation.h computeUpAlg.h computeDownAlg.h computeCounts.h \
+ treeIt.h fromCountTableComponentToDistance.h
+bblEMfixRoot.o bblEMfixRoot.debug.o: bblEMfixRoot.cpp bblEMfixRoot.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h sequenceContainer.h sequence.h \
+ alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ unObservableData.h likelihoodComputation.h computeUpAlg.h \
+ computeDownAlg.h computeCounts.h treeIt.h \
+ fromCountTableComponentToDistancefixRoot.h
+bblEMProprtional.o bblEMProprtional.debug.o: bblEMProprtional.cpp bblEM.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h sequenceContainer.h sequence.h \
+ alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ unObservableData.h bblEMProportional.h likelihoodComputation.h \
+ computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \
+ fromCountTableComponentToDistance.h \
+ fromCountTableComponentToDistanceProp.h
+bblEMProportionalEB.o bblEMProportionalEB.debug.o: bblEMProportionalEB.cpp bblEM.h definitions.h \
+ tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ unObservableData.h bblEMProportionalEB.h likelihoodComputation.h \
+ computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \
+ fromCountTableComponentToDistance.h \
+ fromCountTableComponentToDistancePropEB.h
+bblLSProportionalEB.o bblLSProportionalEB.debug.o: bblLSProportionalEB.cpp bblLSProportionalEB.h \
+ definitions.h tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h likelihoodComputation.h computePijComponent.h \
+ suffStatComponent.h unObservableData.h numRec.h uniformDistribution.h
+bblEMSeperate.o bblEMSeperate.debug.o: bblEMSeperate.cpp bblEM.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h sequenceContainer.h sequence.h \
+ alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ unObservableData.h bblEMSeperate.h
+chebyshevAccelerator.o chebyshevAccelerator.debug.o: chebyshevAccelerator.cpp chebyshevAccelerator.h \
+ pijAccelerator.h definitions.h replacementModel.h
+clustalFormat.o clustalFormat.debug.o: clustalFormat.cpp clustalFormat.h sequenceContainer.h \
+ definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \
+ logFile.h gainLossAlphabet.h codon.h geneticCodeHolder.h
+codon.o codon.debug.o: codon.cpp codon.h definitions.h errorMsg.h someUtil.h logFile.h \
+ alphabet.h geneticCodeHolder.h nucleotide.h amino.h matrixUtils.h \
+ sequenceContainer.h sequence.h mulAlphabet.h gainLossAlphabet.h
+codonJC.o codonJC.debug.o: codonJC.cpp codonJC.h replacementModel.h definitions.h
+computeCounts.o computeCounts.debug.o: computeCounts.cpp computeCounts.h definitions.h \
+ countTableComponent.h sequenceContainer.h sequence.h errorMsg.h \
+ alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h \
+ computePijComponent.h tree.h readTree.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h suffStatComponent.h
+computeDownAlg.o computeDownAlg.debug.o: computeDownAlg.cpp definitions.h computeDownAlg.h \
+ tree.h readTree.h errorMsg.h logFile.h suffStatComponent.h \
+ sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \
+ gainLossAlphabet.h computePijComponent.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h treeIt.h
+computeMarginalAlg.o computeMarginalAlg.debug.o: computeMarginalAlg.cpp definitions.h treeIt.h \
+ errorMsg.h tree.h readTree.h logFile.h computeMarginalAlg.h \
+ suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h
+computePijComponent.o computePijComponent.debug.o: computePijComponent.cpp definitions.h treeIt.h \
+ errorMsg.h tree.h readTree.h logFile.h computePijComponent.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h
+computeUpAlg.o computeUpAlg.debug.o: computeUpAlg.cpp definitions.h computeUpAlg.h tree.h \
+ readTree.h errorMsg.h logFile.h suffStatComponent.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ computePijComponent.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h treeIt.h \
+ seqContainerTreeMap.h
+computeUpAlgFactors.o computeUpAlgFactors.debug.o: computeUpAlgFactors.cpp definitions.h \
+ computeUpAlg.h tree.h readTree.h errorMsg.h logFile.h \
+ suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h seqContainerTreeMap.h treeIt.h
+computeSubstitutionCounts.o computeSubstitutionCounts.debug.o: computeSubstitutionCounts.cpp \
+ computeSubstitutionCounts.h definitions.h replacementModel.h \
+ sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \
+ computePosteriorExpectationOfSubstitutions.h simulateJumps.h \
+ simulateJumpsAbstract.h stochasticProcess.h pijAccelerator.h \
+ distribution.h suffStatComponent.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h \
+ computePosteriorExpectationOfSubstitutions_nonReversibleSp.h \
+ matrixUtils.h simulateCodonsJumps.h codon.h geneticCodeHolder.h treeIt.h \
+ treeUtil.h
+computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.debug.o: \
+ computePosteriorExpectationOfSubstitutions.cpp \
+ computePosteriorExpectationOfSubstitutions.h definitions.h \
+ simulateJumps.h simulateJumpsAbstract.h tree.h readTree.h errorMsg.h \
+ logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h alphabet.h sequenceContainer.h sequence.h mulAlphabet.h \
+ someUtil.h gainLossAlphabet.h suffStatComponent.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h computeDownAlg.h computeUpAlg.h matrixUtils.h \
+ treeIt.h likelihoodComputation.h unObservableData.h
+computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.debug.o: \
+ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp \
+ definitions.h computeDownAlg.h tree.h readTree.h errorMsg.h logFile.h \
+ suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h computeUpAlg.h matrixUtils.h treeIt.h \
+ likelihoodComputation.h unObservableData.h \
+ computePosteriorExpectationOfSubstitutions_nonReversibleSp.h \
+ computePosteriorExpectationOfSubstitutions.h simulateJumps.h \
+ simulateJumpsAbstract.h
+ConversionUtils.o ConversionUtils.debug.o: ConversionUtils.cpp ConversionUtils.h definitions.h \
+ someUtil.h logFile.h alphabet.h errorMsg.h
+countTableComponent.o countTableComponent.debug.o: countTableComponent.cpp countTableComponent.h \
+ definitions.h logFile.h
+datMatrixHolder.o datMatrixHolder.debug.o: datMatrixHolder.cpp datMatrixHolder.h cpREV45.dat.q \
+ dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q \
+ adrianCodon.dat.q LG.dat.q
+distanceTable.o distanceTable.debug.o: distanceTable.cpp definitions.h distanceTable.h \
+ distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h sequenceContainer.h gainLossAlphabet.h
+distribution.o distribution.debug.o: distribution.cpp distribution.h definitions.h errorMsg.h
+errorMsg.o errorMsg.debug.o: errorMsg.cpp definitions.h errorMsg.h logFile.h
+evaluateCharacterFreq.o evaluateCharacterFreq.debug.o: evaluateCharacterFreq.cpp \
+ evaluateCharacterFreq.h sequenceContainer.h definitions.h sequence.h \
+ errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ gainLossAlphabet.h
+fastStartTree.o fastStartTree.debug.o: fastStartTree.cpp definitions.h tree.h readTree.h \
+ errorMsg.h logFile.h treeUtil.h fastStartTree.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ bblEM.h countTableComponent.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h suffStatComponent.h unObservableData.h \
+ likeDist.h distanceMethod.h jcDistance.h likelihoodComputation.h \
+ getRandomWeights.h distanceTable.h nj.h njConstrain.h distances2Tree.h
+fastaFormat.o fastaFormat.debug.o: fastaFormat.cpp fastaFormat.h sequenceContainer.h \
+ definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \
+ logFile.h gainLossAlphabet.h ConversionUtils.h
+findRateOfGene.o findRateOfGene.debug.o: findRateOfGene.cpp definitions.h findRateOfGene.h \
+ numRec.h errorMsg.h uniformDistribution.h distribution.h logFile.h \
+ likelihoodComputation.h computePijComponent.h tree.h readTree.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h suffStatComponent.h \
+ unObservableData.h computeUpAlg.h
+fromCountTableComponentToDistance.o fromCountTableComponentToDistance.debug.o: \
+ fromCountTableComponentToDistance.cpp \
+ fromCountTableComponentToDistance.h definitions.h countTableComponent.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ unObservableData.h tree.h readTree.h errorMsg.h logFile.h \
+ sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \
+ gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h likeDist.h \
+ distanceMethod.h jcDistance.h
+fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.debug.o: \
+ fromCountTableComponentToDistancefixRoot.cpp \
+ fromCountTableComponentToDistancefixRoot.h definitions.h \
+ countTableComponent.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h unObservableData.h tree.h readTree.h \
+ errorMsg.h logFile.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h likeDistfixRoot.h distanceMethod.h \
+ jcDistance.h
+fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.debug.o: \
+ fromCountTableComponentToDistanceProp.cpp \
+ fromCountTableComponentToDistanceProp.h definitions.h \
+ countTableComponent.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h likeDistProp.h
+fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.debug.o: \
+ fromCountTableComponentToDistancePropEB.cpp \
+ fromCountTableComponentToDistancePropEB.h definitions.h \
+ countTableComponent.h multipleStochasticProcess.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \
+ generalGammaDistribution.h errorMsg.h likeDistPropEB.h logFile.h
+fromQtoPt.o fromQtoPt.debug.o: fromQtoPt.cpp definitions.h fromQtoPt.h replacementModel.h \
+ errorMsg.h numRec.h uniformDistribution.h distribution.h logFile.h \
+ matrixUtils.h
+generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.debug.o: \
+ generalGammaDistributionFixedCategories.cpp \
+ generalGammaDistributionFixedCategories.h definitions.h \
+ generalGammaDistribution.h distribution.h errorMsg.h gammaUtilities.h \
+ numRec.h uniformDistribution.h logFile.h
+gammaDistribution.o gammaDistribution.debug.o: gammaDistribution.cpp definitions.h \
+ gammaDistribution.h generalGammaDistribution.h distribution.h errorMsg.h \
+ gammaUtilities.h numRec.h uniformDistribution.h logFile.h
+gammaUtilities.o gammaUtilities.debug.o: gammaUtilities.cpp gammaUtilities.h definitions.h \
+ numRec.h errorMsg.h uniformDistribution.h distribution.h logFile.h
+generalGammaDistribution.o generalGammaDistribution.debug.o: generalGammaDistribution.cpp \
+ generalGammaDistribution.h definitions.h distribution.h gammaUtilities.h \
+ numRec.h errorMsg.h uniformDistribution.h logFile.h
+getRandomWeights.o getRandomWeights.debug.o: getRandomWeights.cpp getRandomWeights.h definitions.h \
+ talRandom.h logFile.h
+goldmanYangModel.o goldmanYangModel.debug.o: goldmanYangModel.cpp goldmanYangModel.h definitions.h \
+ replacementModel.h fromQtoPt.h granthamChemicalDistances.h codon.h \
+ errorMsg.h someUtil.h logFile.h alphabet.h geneticCodeHolder.h \
+ readDatMatrix.h datMatrixHolder.h
+granthamChemicalDistances.o granthamChemicalDistances.debug.o: granthamChemicalDistances.cpp \
+ granthamChemicalDistances.h definitions.h
+hky.o hky.debug.o: hky.cpp hky.h replacementModel.h definitions.h errorMsg.h
+simulateWithDependence.o simulateWithDependence.debug.o: simulateWithDependence.cpp \
+ simulateWithDependence.h tree.h definitions.h readTree.h errorMsg.h \
+ logFile.h alphabet.h nucleotide.h simulateTree.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ trivialAccelerator.h uniDistribution.h \
+ generalGammaDistributionPlusInvariant.h distributionPlusInvariant.h \
+ generalGammaDistribution.h gammaUtilities.h numRec.h \
+ uniformDistribution.h fastaFormat.h gtrModel.h fromQtoPt.h
+KH_calculation.o KH_calculation.debug.o: KH_calculation.cpp KH_calculation.h definitions.h
+likeDist.o likeDist.debug.o: likeDist.cpp likeDist.h definitions.h countTableComponent.h \
+ distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h jcDistance.h unObservableData.h tree.h \
+ readTree.h sequenceContainer.h gainLossAlphabet.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h numRec.h uniformDistribution.h
+likeDistfixRoot.o likeDistfixRoot.debug.o: likeDistfixRoot.cpp likeDistfixRoot.h definitions.h \
+ countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h jcDistance.h sequenceContainer.h \
+ gainLossAlphabet.h unObservableData.h tree.h readTree.h \
+ computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h numRec.h uniformDistribution.h
+likeDistProp.o likeDistProp.debug.o: likeDistProp.cpp likeDistProp.h definitions.h \
+ countTableComponent.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h numRec.h errorMsg.h \
+ uniformDistribution.h logFile.h
+likeDistPropEB.o likeDistPropEB.debug.o: likeDistPropEB.cpp likeDistPropEB.h definitions.h \
+ countTableComponent.h multipleStochasticProcess.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \
+ generalGammaDistribution.h errorMsg.h logFile.h numRec.h \
+ uniformDistribution.h
+likelihoodComputation.o likelihoodComputation.debug.o: likelihoodComputation.cpp definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h computeUpAlg.h suffStatComponent.h \
+ sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \
+ gainLossAlphabet.h computePijComponent.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h likelihoodComputation.h unObservableData.h \
+ gammaUtilities.h numRec.h uniformDistribution.h
+likelihoodComputationFactors.o likelihoodComputationFactors.debug.o: likelihoodComputationFactors.cpp \
+ definitions.h tree.h readTree.h errorMsg.h logFile.h computeUpAlg.h \
+ suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \
+ mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h likelihoodComputationFactors.h
+logFile.o logFile.debug.o: logFile.cpp logFile.h errorMsg.h
+maseFormat.o maseFormat.debug.o: maseFormat.cpp maseFormat.h sequenceContainer.h \
+ definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \
+ logFile.h gainLossAlphabet.h
+molphyFormat.o molphyFormat.debug.o: molphyFormat.cpp molphyFormat.h sequenceContainer.h \
+ definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \
+ logFile.h gainLossAlphabet.h
+nexusFormat.o nexusFormat.debug.o: nexusFormat.cpp nexusFormat.h sequenceContainer.h \
+ definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \
+ logFile.h gainLossAlphabet.h
+nj.o nj.debug.o: nj.cpp nj.h definitions.h tree.h readTree.h errorMsg.h logFile.h \
+ sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \
+ gainLossAlphabet.h njConstrain.h distances2Tree.h treeUtil.h
+njConstrain.o njConstrain.debug.o: njConstrain.cpp definitions.h njConstrain.h \
+ sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h
+nucJC.o nucJC.debug.o: nucJC.cpp nucJC.h replacementModel.h definitions.h
+nucleotide.o nucleotide.debug.o: nucleotide.cpp nucleotide.h definitions.h alphabet.h \
+ errorMsg.h
+numRec.o numRec.debug.o: numRec.cpp numRec.h definitions.h errorMsg.h \
+ uniformDistribution.h distribution.h logFile.h matrixUtils.h
+Parameters.o Parameters.debug.o: Parameters.cpp Parameters.h ConversionUtils.h definitions.h
+phylipFormat.o phylipFormat.debug.o: phylipFormat.cpp phylipFormat.h definitions.h \
+ sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h gainLossAlphabet.h
+pijAccelerator.o pijAccelerator.debug.o: pijAccelerator.cpp pijAccelerator.h definitions.h \
+ replacementModel.h
+readDatMatrix.o readDatMatrix.debug.o: readDatMatrix.cpp readDatMatrix.h definitions.h \
+ datMatrixHolder.h replacementModel.h errorMsg.h logFile.h fromQtoPt.h
+readTree.o readTree.debug.o: readTree.cpp definitions.h errorMsg.h someUtil.h logFile.h \
+ alphabet.h readTree.h
+recognizeFormat.o recognizeFormat.debug.o: recognizeFormat.cpp recognizeFormat.h \
+ sequenceContainer.h definitions.h sequence.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h maseFormat.h \
+ molphyFormat.h phylipFormat.h nexusFormat.h fastaFormat.h \
+ clustalFormat.h phylipSequentialFormat.h
+replacementModel.o replacementModel.debug.o: replacementModel.cpp replacementModel.h definitions.h
+searchStatus.o searchStatus.debug.o: searchStatus.cpp searchStatus.h definitions.h
+seqContainerTreeMap.o seqContainerTreeMap.debug.o: seqContainerTreeMap.cpp seqContainerTreeMap.h \
+ definitions.h tree.h readTree.h errorMsg.h logFile.h treeIt.h \
+ sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \
+ gainLossAlphabet.h treeUtil.h
+sequence.o sequence.debug.o: sequence.cpp sequence.h definitions.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h
+sequenceContainer.o sequenceContainer.debug.o: sequenceContainer.cpp sequenceContainer.h \
+ definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \
+ logFile.h gainLossAlphabet.h fastaFormat.h
+simulateTree.o simulateTree.debug.o: simulateTree.cpp definitions.h treeUtil.h tree.h \
+ readTree.h errorMsg.h logFile.h simulateTree.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ talRandom.h gammaDistribution.h generalGammaDistribution.h codon.h \
+ geneticCodeHolder.h
+siteSpecificRate.o siteSpecificRate.debug.o: siteSpecificRate.cpp siteSpecificRate.h definitions.h \
+ tree.h readTree.h errorMsg.h logFile.h sequenceContainer.h sequence.h \
+ alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ multipleStochasticProcess.h computePijComponent.h gammaDistribution.h \
+ generalGammaDistribution.h unObservableData.h numRec.h \
+ uniformDistribution.h checkcovFanctors.h likelihoodComputation.h \
+ suffStatComponent.h
+someUtil.o someUtil.debug.o: someUtil.cpp someUtil.h logFile.h definitions.h alphabet.h \
+ errorMsg.h talRandom.h
+split.o split.debug.o: split.cpp split.h definitions.h
+splitMap.o splitMap.debug.o: splitMap.cpp splitMap.h definitions.h split.h
+splitTreeUtil.o splitTreeUtil.debug.o: splitTreeUtil.cpp splitTreeUtil.h tree.h definitions.h \
+ readTree.h errorMsg.h logFile.h split.h someUtil.h alphabet.h
+stochasticProcess.o stochasticProcess.debug.o: stochasticProcess.cpp stochasticProcess.h \
+ pijAccelerator.h definitions.h replacementModel.h distribution.h \
+ errorMsg.h
+suffStatComponent.o suffStatComponent.debug.o: suffStatComponent.cpp suffStatComponent.h \
+ definitions.h
+talRandom.o talRandom.debug.o: talRandom.cpp talRandom.h definitions.h logFile.h
+tree.o tree.debug.o: tree.cpp definitions.h tree.h readTree.h errorMsg.h logFile.h \
+ treeUtil.h someUtil.h alphabet.h
+treeIt.o treeIt.debug.o: treeIt.cpp definitions.h treeIt.h errorMsg.h tree.h readTree.h \
+ logFile.h
+treeUtil.o treeUtil.debug.o: treeUtil.cpp definitions.h treeUtil.h tree.h readTree.h \
+ errorMsg.h logFile.h treeIt.h someUtil.h alphabet.h
+uniDistribution.o uniDistribution.debug.o: uniDistribution.cpp uniDistribution.h distribution.h \
+ definitions.h errorMsg.h
+uniformDistribution.o uniformDistribution.debug.o: uniformDistribution.cpp uniformDistribution.h \
+ definitions.h distribution.h
+cmdline2EvolObjs.o cmdline2EvolObjs.debug.o: cmdline2EvolObjs.cpp cmdline2EvolObjs.h amino.h \
+ definitions.h errorMsg.h alphabet.h geneticCodeHolder.h codon.h \
+ someUtil.h logFile.h nucleotide.h sequenceContainer.h sequence.h \
+ mulAlphabet.h gainLossAlphabet.h tree.h readTree.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h uniDistribution.h \
+ trivialAccelerator.h alphaTrivialAccelerator.h readDatMatrix.h \
+ datMatrixHolder.h chebyshevAccelerator.h talRandom.h nucJC.h aaJC.h \
+ hky.h tamura92.h gtrModel.h fromQtoPt.h gammaDistribution.h \
+ generalGammaDistribution.h recognizeFormat.h replacementModelSSRV.h \
+ stochasticProcessSSRV.h
+generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.debug.o: generalGammaDistributionLaguerre.cpp \
+ generalGammaDistributionLaguerre.h definitions.h \
+ generalGammaDistribution.h distribution.h gammaUtilities.h numRec.h \
+ errorMsg.h uniformDistribution.h logFile.h GLaguer.h
+gammaDistributionLaguerre.o gammaDistributionLaguerre.debug.o: gammaDistributionLaguerre.cpp \
+ gammaDistributionLaguerre.h definitions.h \
+ generalGammaDistributionLaguerre.h generalGammaDistribution.h \
+ distribution.h errorMsg.h gammaUtilities.h numRec.h \
+ uniformDistribution.h logFile.h
+GLaguer.o GLaguer.debug.o: GLaguer.cpp definitions.h GLaguer.h errorMsg.h \
+ gammaUtilities.h numRec.h uniformDistribution.h distribution.h logFile.h
+givenRatesMLDistance.o givenRatesMLDistance.debug.o: givenRatesMLDistance.cpp givenRatesMLDistance.h \
+ definitions.h countTableComponent.h likeDist.h distanceMethod.h \
+ sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \
+ gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h numRec.h \
+ uniformDistribution.h
+distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.debug.o: distanceBasedSeqs2Tree.cpp \
+ distanceBasedSeqs2Tree.h distanceMethod.h definitions.h sequence.h \
+ errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ sequenceContainer.h gainLossAlphabet.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h likeDist.h \
+ countTableComponent.h jcDistance.h unObservableData.h tree.h readTree.h \
+ computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h distances2Tree.h givenRatesMLDistance.h \
+ posteriorDistance.h uniDistribution.h distanceTable.h bestAlpha.h \
+ likelihoodComputation.h suffStatComponent.h siteSpecificRate.h bblEM.h \
+ tamura92.h bestTamura92param.h bestGtrModelParams.h gtrModel.h \
+ fromQtoPt.h replacementModelSSRV.h trivialAccelerator.h
+posteriorDistance.o posteriorDistance.debug.o: posteriorDistance.cpp posteriorDistance.h likeDist.h \
+ definitions.h countTableComponent.h distanceMethod.h sequence.h \
+ errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \
+ jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \
+ gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h numRec.h \
+ uniformDistribution.h uniDistribution.h
+pairwiseGammaDistance.o pairwiseGammaDistance.debug.o: pairwiseGammaDistance.cpp \
+ pairwiseGammaDistance.h likeDist.h definitions.h countTableComponent.h \
+ distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h jcDistance.h unObservableData.h tree.h \
+ readTree.h sequenceContainer.h gainLossAlphabet.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h numRec.h uniformDistribution.h \
+ uniDistribution.h
+doubleRep.o doubleRep.debug.o: doubleRep.cpp
+logRep.o logRep.debug.o: logRep.cpp
+indel.o indel.debug.o: indel.cpp indel.h definitions.h errorMsg.h alphabet.h
+indelModel.o indelModel.debug.o: indelModel.cpp indelModel.h replacementModel.h \
+ definitions.h
+mulAlphabet.o mulAlphabet.debug.o: mulAlphabet.cpp mulAlphabet.h definitions.h alphabet.h \
+ someUtil.h logFile.h distribution.h errorMsg.h
+replacementModelSSRV.o replacementModelSSRV.debug.o: replacementModelSSRV.cpp replacementModelSSRV.h \
+ replacementModel.h definitions.h distribution.h fromQtoPt.h errorMsg.h \
+ logFile.h
+stochasticProcessSSRV.o stochasticProcessSSRV.debug.o: stochasticProcessSSRV.cpp \
+ stochasticProcessSSRV.h stochasticProcess.h pijAccelerator.h \
+ definitions.h replacementModel.h distribution.h replacementModelSSRV.h \
+ fromQtoPt.h errorMsg.h
+bestAlphaAndNu.o bestAlphaAndNu.debug.o: bestAlphaAndNu.cpp bestAlphaAndNu.h definitions.h \
+ sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h gainLossAlphabet.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \
+ generalGammaDistribution.h tree.h readTree.h replacementModelSSRV.h \
+ fromQtoPt.h tamura92.h stochasticProcessSSRV.h C_evalParamUSSRV.h \
+ likelihoodComputation.h computePijComponent.h \
+ multipleStochasticProcess.h suffStatComponent.h unObservableData.h \
+ likelihoodComputation2USSRV.h ussrvModel.h computeUpAlg.h bestAlpha.h \
+ numRec.h uniformDistribution.h bblEM.h countTableComponent.h
+C_evalParamUSSRV.o C_evalParamUSSRV.debug.o: C_evalParamUSSRV.cpp C_evalParamUSSRV.h definitions.h \
+ likelihoodComputation.h computePijComponent.h tree.h readTree.h \
+ errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h unObservableData.h likelihoodComputation2USSRV.h \
+ ussrvModel.h stochasticProcessSSRV.h replacementModelSSRV.h fromQtoPt.h \
+ computeUpAlg.h tamura92.h
+matrixUtils.o matrixUtils.debug.o: matrixUtils.cpp matrixUtils.h definitions.h logFile.h \
+ errorMsg.h
+betaOmegaDistribution.o betaOmegaDistribution.debug.o: betaOmegaDistribution.cpp \
+ betaOmegaDistribution.h definitions.h distribution.h betaDistribution.h \
+ logFile.h gammaUtilities.h numRec.h errorMsg.h uniformDistribution.h \
+ betaUtilities.h
+betaUtilities.o betaUtilities.debug.o: betaUtilities.cpp definitions.h betaUtilities.h numRec.h \
+ errorMsg.h uniformDistribution.h distribution.h logFile.h \
+ gammaUtilities.h
+betaDistribution.o betaDistribution.debug.o: betaDistribution.cpp betaDistribution.h definitions.h \
+ distribution.h gammaUtilities.h numRec.h errorMsg.h \
+ uniformDistribution.h logFile.h betaUtilities.h
+geneticCodeHolder.o geneticCodeHolder.debug.o: geneticCodeHolder.cpp geneticCodeHolder.h \
+ replacementMatrixSource/nuclearStandard.code \
+ replacementMatrixSource/nuclearEuplotid.code \
+ replacementMatrixSource/nuclearCiliate.code \
+ replacementMatrixSource/nuclearBlepharisma.code \
+ replacementMatrixSource/mitochondriaYeast.code \
+ replacementMatrixSource/mitochondriaVertebrate.code \
+ replacementMatrixSource/mitochondriaProtozoan.code \
+ replacementMatrixSource/mitochondriaInvertebrate.code \
+ replacementMatrixSource/mitochondriaFlatworm.code \
+ replacementMatrixSource/mitochondriaEchinoderm.code \
+ replacementMatrixSource/mitochondriaAscidian.code
+samplingSequences.o samplingSequences.debug.o: samplingSequences.cpp samplingSequences.h \
+ definitions.h distanceMethod.h sequence.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h sequenceContainer.h \
+ gainLossAlphabet.h pDistance.h talRandom.h
+bblEM2USSRV.o bblEM2USSRV.debug.o: bblEM2USSRV.cpp bblEM2USSRV.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h sequenceContainer.h sequence.h \
+ alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ ussrvModel.h stochasticProcessSSRV.h replacementModelSSRV.h fromQtoPt.h \
+ computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \
+ fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h \
+ distanceMethod.h likelihoodComputation2USSRV.h likelihoodComputation.h \
+ unObservableData.h
+bestParamUSSRV.o bestParamUSSRV.debug.o: bestParamUSSRV.cpp bestParamUSSRV.h definitions.h \
+ sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h gainLossAlphabet.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \
+ generalGammaDistribution.h tree.h readTree.h replacementModelSSRV.h \
+ fromQtoPt.h stochasticProcessSSRV.h C_evalParamUSSRV.h \
+ likelihoodComputation.h computePijComponent.h \
+ multipleStochasticProcess.h suffStatComponent.h unObservableData.h \
+ likelihoodComputation2USSRV.h ussrvModel.h computeUpAlg.h tamura92.h \
+ bestAlpha.h numRec.h uniformDistribution.h bblEM.h countTableComponent.h \
+ bestAlphaAndNu.h bblEM2USSRV.h computeDownAlg.h computeCounts.h treeIt.h \
+ fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h \
+ distanceMethod.h
+likeDist2USSRV.o likeDist2USSRV.debug.o: likeDist2USSRV.cpp likeDist2USSRV.h definitions.h \
+ countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h ussrvModel.h stochasticProcessSSRV.h \
+ replacementModelSSRV.h fromQtoPt.h gammaDistribution.h \
+ generalGammaDistribution.h numRec.h uniformDistribution.h
+ussrvModel.o ussrvModel.debug.o: ussrvModel.cpp ussrvModel.h stochasticProcessSSRV.h \
+ stochasticProcess.h pijAccelerator.h definitions.h replacementModel.h \
+ distribution.h replacementModelSSRV.h fromQtoPt.h errorMsg.h \
+ gammaDistribution.h generalGammaDistribution.h logFile.h
+likelihoodComputation2USSRV.o likelihoodComputation2USSRV.debug.o: likelihoodComputation2USSRV.cpp \
+ likelihoodComputation2USSRV.h definitions.h computePijComponent.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h ussrvModel.h stochasticProcessSSRV.h \
+ replacementModelSSRV.h fromQtoPt.h computeUpAlg.h \
+ likelihoodComputation.h unObservableData.h
+fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.debug.o: \
+ fromCountTableComponentToDistance2USSRV.cpp \
+ fromCountTableComponentToDistance2USSRV.h definitions.h \
+ countTableComponent.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h ussrvModel.h stochasticProcessSSRV.h \
+ replacementModelSSRV.h fromQtoPt.h errorMsg.h gammaDistribution.h \
+ generalGammaDistribution.h logFile.h likeDist2USSRV.h distanceMethod.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h likeDist.h jcDistance.h \
+ unObservableData.h tree.h readTree.h sequenceContainer.h \
+ gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h
+normalDist.o normalDist.debug.o: normalDist.cpp normalDist.h definitions.h
+tamura92.o tamura92.debug.o: tamura92.cpp tamura92.h replacementModel.h definitions.h \
+ errorMsg.h
+bestTamura92param.o bestTamura92param.debug.o: bestTamura92param.cpp bestTamura92param.h \
+ definitions.h likelihoodComputation.h computePijComponent.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h unObservableData.h tamura92.h bblEM.h \
+ countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \
+ numRec.h uniformDistribution.h bestAlpha.h
+phylipSequentialFormat.o phylipSequentialFormat.debug.o: phylipSequentialFormat.cpp \
+ phylipSequentialFormat.h definitions.h sequenceContainer.h sequence.h \
+ errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ gainLossAlphabet.h
+simulateCodonsJumps.o simulateCodonsJumps.debug.o: simulateCodonsJumps.cpp simulateCodonsJumps.h \
+ simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \
+ logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h alphabet.h codon.h someUtil.h geneticCodeHolder.h \
+ talRandom.h
+simulateJumpsAbstract.o simulateJumpsAbstract.debug.o: simulateJumpsAbstract.cpp \
+ simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \
+ logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h alphabet.h
+ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.debug.o: ssrvDistanceSeqs2Tree.cpp \
+ ssrvDistanceSeqs2Tree.h distanceBasedSeqs2Tree.h distanceMethod.h \
+ definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \
+ logFile.h sequenceContainer.h gainLossAlphabet.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h likeDist.h \
+ countTableComponent.h jcDistance.h unObservableData.h tree.h readTree.h \
+ computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h distances2Tree.h givenRatesMLDistance.h \
+ posteriorDistance.h bestParamUSSRV.h replacementModelSSRV.h fromQtoPt.h \
+ stochasticProcessSSRV.h C_evalParamUSSRV.h likelihoodComputation.h \
+ suffStatComponent.h likelihoodComputation2USSRV.h ussrvModel.h \
+ computeUpAlg.h tamura92.h bestAlpha.h numRec.h uniformDistribution.h \
+ bblEM.h bestAlphaAndNu.h bblEM2USSRV.h computeDownAlg.h computeCounts.h \
+ treeIt.h fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h
+multipleStochasticProcess.o multipleStochasticProcess.debug.o: multipleStochasticProcess.cpp \
+ multipleStochasticProcess.h stochasticProcess.h pijAccelerator.h \
+ definitions.h replacementModel.h distribution.h errorMsg.h
+distributionPlusInvariant.o distributionPlusInvariant.debug.o: distributionPlusInvariant.cpp definitions.h \
+ distributionPlusInvariant.h distribution.h errorMsg.h logFile.h
+extremeValDistribution.o extremeValDistribution.debug.o: extremeValDistribution.cpp \
+ extremeValDistribution.h definitions.h
+gammaDistributionFixedCategories.o gammaDistributionFixedCategories.debug.o: gammaDistributionFixedCategories.cpp \
+ gammaDistributionFixedCategories.h definitions.h \
+ generalGammaDistributionFixedCategories.h generalGammaDistribution.h \
+ distribution.h errorMsg.h gammaUtilities.h numRec.h \
+ uniformDistribution.h logFile.h matrixUtils.h
+generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.debug.o: \
+ generalGammaDistributionPlusInvariant.cpp \
+ generalGammaDistributionPlusInvariant.h definitions.h \
+ distributionPlusInvariant.h distribution.h generalGammaDistribution.h \
+ errorMsg.h gammaUtilities.h numRec.h uniformDistribution.h logFile.h
+gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.debug.o: gammaDistributionPlusInvariant.cpp \
+ gammaDistributionPlusInvariant.h definitions.h \
+ distributionPlusInvariant.h distribution.h gammaDistribution.h \
+ generalGammaDistribution.h errorMsg.h gammaUtilities.h numRec.h \
+ uniformDistribution.h logFile.h
+distributionPlusCategory.o distributionPlusCategory.debug.o: distributionPlusCategory.cpp \
+ distributionPlusCategory.h definitions.h distribution.h logFile.h \
+ errorMsg.h
+simulateJumps.o simulateJumps.debug.o: simulateJumps.cpp simulateJumps.h \
+ simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \
+ logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h alphabet.h talRandom.h someUtil.h
+computeJumps.o computeJumps.debug.o: computeJumps.cpp computeJumps.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h alphabet.h someUtil.h talRandom.h \
+ matrixUtils.h
+seqeuncesFilter.o seqeuncesFilter.debug.o: seqeuncesFilter.cpp seqeuncesFilter.h definitions.h \
+ sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \
+ someUtil.h logFile.h gainLossAlphabet.h codon.h geneticCodeHolder.h \
+ amino.h fastaFormat.h nucleotide.h
+optGammaMixtureLS.o optGammaMixtureLS.debug.o: optGammaMixtureLS.cpp optGammaMixtureLS.h \
+ definitions.h suffStatGammaMixture.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ gainLossAlphabet.h tree.h readTree.h mixtureDistribution.h \
+ generalGammaDistribution.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h gammaUtilities.h \
+ numRec.h uniformDistribution.h likelihoodComputation.h \
+ suffStatComponent.h unObservableData.h
+mixtureDistribution.o mixtureDistribution.debug.o: mixtureDistribution.cpp mixtureDistribution.h \
+ definitions.h generalGammaDistribution.h distribution.h \
+ generalGammaDistributionLaguerre.h talRandom.h logFile.h someUtil.h \
+ alphabet.h errorMsg.h
+suffStatGammaMixture.o suffStatGammaMixture.debug.o: suffStatGammaMixture.cpp suffStatGammaMixture.h \
+ definitions.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h sequenceContainer.h sequence.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \
+ mixtureDistribution.h generalGammaDistribution.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h likelihoodComputation.h \
+ suffStatComponent.h unObservableData.h gammaUtilities.h numRec.h \
+ uniformDistribution.h uniDistribution.h
+GamMixtureOptimizer.o GamMixtureOptimizer.debug.o: GamMixtureOptimizer.cpp GamMixtureOptimizer.h \
+ definitions.h stochasticProcess.h pijAccelerator.h replacementModel.h \
+ distribution.h sequenceContainer.h sequence.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \
+ mixtureDistribution.h generalGammaDistribution.h unObservableData.h \
+ computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \
+ optGammaMixtureEM.h suffStatGammaMixture.h gammaUtilities.h numRec.h \
+ uniformDistribution.h optGammaMixtureLS.h likelihoodComputation.h \
+ suffStatComponent.h
+optGammaMixtureEM.o optGammaMixtureEM.debug.o: optGammaMixtureEM.cpp optGammaMixtureEM.h \
+ definitions.h suffStatGammaMixture.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ gainLossAlphabet.h tree.h readTree.h mixtureDistribution.h \
+ generalGammaDistribution.h computePijComponent.h \
+ multipleStochasticProcess.h gammaDistribution.h gammaUtilities.h \
+ numRec.h uniformDistribution.h likelihoodComputation.h \
+ suffStatComponent.h unObservableData.h uniDistribution.h
+gainLossAlphabet.o gainLossAlphabet.debug.o: gainLossAlphabet.cpp gainLossAlphabet.h alphabet.h \
+ errorMsg.h
+wYangModel.o wYangModel.debug.o: wYangModel.cpp wYangModel.h replacementModel.h \
+ definitions.h fromQtoPt.h codon.h errorMsg.h someUtil.h logFile.h \
+ alphabet.h geneticCodeHolder.h readDatMatrix.h datMatrixHolder.h
+codonUtils.o codonUtils.debug.o: codonUtils.cpp codonUtils.h nucleotide.h definitions.h \
+ alphabet.h codon.h errorMsg.h someUtil.h logFile.h geneticCodeHolder.h \
+ amino.h fastaFormat.h sequenceContainer.h sequence.h mulAlphabet.h \
+ gainLossAlphabet.h clustalFormat.h recognizeFormat.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h wYangModel.h \
+ fromQtoPt.h evaluateCharacterFreq.h numRec.h uniformDistribution.h
+likelihoodComputation2Codon.o likelihoodComputation2Codon.debug.o: likelihoodComputation2Codon.cpp \
+ likelihoodComputation2Codon.h definitions.h computePijComponent.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h \
+ computeUpAlg.h likelihoodComputation.h unObservableData.h
+likeDist2Codon.o likeDist2Codon.debug.o: likeDist2Codon.cpp likeDist2Codon.h definitions.h \
+ countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \
+ mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h wYangModel.h fromQtoPt.h codon.h \
+ geneticCodeHolder.h numRec.h uniformDistribution.h
+unObservableData.o unObservableData.debug.o: unObservableData.cpp unObservableData.h definitions.h \
+ tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \
+ pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \
+ generalGammaDistribution.h likelihoodComputation.h suffStatComponent.h \
+ likelihoodComputationGL.h computeUpAlg.h
+likelihoodComputationGL.o likelihoodComputationGL.debug.o: likelihoodComputationGL.cpp \
+ likelihoodComputationGL.h definitions.h computePijComponent.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h unObservableData.h computeUpAlg.h \
+ likelihoodComputation.h
+threeStateModel.o threeStateModel.debug.o: threeStateModel.cpp threeStateModel.h definitions.h \
+ replacementModel.h fromQtoPt.h errorMsg.h matrixUtils.h logFile.h \
+ someUtil.h alphabet.h
+threeStateAlphabet.o threeStateAlphabet.debug.o: threeStateAlphabet.cpp threeStateAlphabet.h \
+ alphabet.h errorMsg.h
+oneTwoMoreModel.o oneTwoMoreModel.debug.o: oneTwoMoreModel.cpp oneTwoMoreModel.h definitions.h \
+ replacementModel.h fromQtoPt.h errorMsg.h matrixUtils.h logFile.h \
+ someUtil.h alphabet.h
+betaDistributionFixedCategories.o betaDistributionFixedCategories.debug.o: betaDistributionFixedCategories.cpp \
+ betaDistributionFixedCategories.h definitions.h betaDistribution.h \
+ distribution.h errorMsg.h gammaUtilities.h numRec.h \
+ uniformDistribution.h logFile.h
+betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.debug.o: \
+ betaDistributionFixedCategoriesWithOmegaUniform.cpp \
+ betaDistributionFixedCategoriesWithOmegaUniform.h definitions.h \
+ betaDistributionFixedCategories.h betaDistribution.h distribution.h \
+ errorMsg.h uniformDistribution.h gammaUtilities.h numRec.h logFile.h \
+ matrixUtils.h
+bblEM2codon.o bblEM2codon.debug.o: bblEM2codon.cpp bblEM2codon.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h sequenceContainer.h sequence.h \
+ alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ countTableComponent.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \
+ likelihoodComputation.h unObservableData.h likelihoodComputation2Codon.h \
+ fromCountTableComponentToDistance2Codon.h computeUpAlg.h \
+ computeDownAlg.h computeCounts.h treeIt.h
+bestAlphaAndK.o bestAlphaAndK.debug.o: bestAlphaAndK.cpp bestAlphaAndK.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h likelihoodComputation.h \
+ computePijComponent.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h unObservableData.h likelihoodComputation2Codon.h \
+ wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h bblEM2codon.h \
+ countTableComponent.h computeUpAlg.h numRec.h uniformDistribution.h \
+ betaOmegaDistribution.h betaDistribution.h codonUtils.h nucleotide.h \
+ amino.h fastaFormat.h clustalFormat.h recognizeFormat.h \
+ evaluateCharacterFreq.h
+fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.debug.o: \
+ fromCountTableComponentToDistance2Codon.cpp \
+ fromCountTableComponentToDistance2Codon.h definitions.h \
+ countTableComponent.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h likeDist2Codon.h distanceMethod.h \
+ sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \
+ wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h likeDist.h \
+ jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \
+ gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h
+gtrModel.o gtrModel.debug.o: gtrModel.cpp gtrModel.h replacementModel.h definitions.h \
+ fromQtoPt.h readDatMatrix.h datMatrixHolder.h errorMsg.h matrixUtils.h \
+ logFile.h
+bestGtrModelParams.o bestGtrModelParams.debug.o: bestGtrModelParams.cpp bestGtrModelParams.h \
+ definitions.h likelihoodComputation.h computePijComponent.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h multipleStochasticProcess.h \
+ gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \
+ sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \
+ suffStatComponent.h unObservableData.h gtrModel.h fromQtoPt.h bblEM.h \
+ countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \
+ numRec.h uniformDistribution.h bestAlpha.h
+simulateRateShiftJumps.o simulateRateShiftJumps.debug.o: simulateRateShiftJumps.cpp \
+ simulateRateShiftJumps.h simulateJumpsAbstract.h definitions.h tree.h \
+ readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \
+ replacementModel.h distribution.h alphabet.h mulAlphabet.h someUtil.h \
+ talRandom.h replacementModelSSRV.h fromQtoPt.h \
+ generalGammaDistribution.h
+integerAlphabet.o integerAlphabet.debug.o: integerAlphabet.cpp integerAlphabet.h alphabet.h \
+ errorMsg.h logFile.h someUtil.h definitions.h


=====================================
libs/phylogeny/someUtil.cpp
=====================================
@@ -1,4 +1,4 @@
-// $Id: someUtil.cpp 11906 2013-12-26 10:12:24Z itaymay $
+// $Id: someUtil.cpp 15479 2016-10-10 16:25:21Z elilevy $
 
 #include "someUtil.h"
 #include "errorMsg.h"
@@ -226,13 +226,17 @@ bool isCharInString(const string& stringToCheck, const char charToCheck) {
 string double2string(const double x, const int lenght, bool round){
 	
 	// first getting the integer part:
-	//Itay: fixing bug regarding negative floats 
 	double x_abs = fabs(x);
 	int theIntegerPart = static_cast<int>(x_abs);
 	double theRemainingPart = fabs(x_abs-theIntegerPart);
 	int integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght));
-	if (round)
+	if (round) {
 		integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght)+0.5);
+		if (integerRepresentingTheRemainingPart == pow(10.0,lenght)) {
+			integerRepresentingTheRemainingPart = 0;
+			theIntegerPart++;
+		}
+	}
 
 	string part1 = int2string(theIntegerPart);
 	string part2 = int2string(integerRepresentingTheRemainingPart);
@@ -353,7 +357,7 @@ MDOUBLE string2double(const string& inString) {
 
 bool checkThatFileExist(const string& fileName) {
 	ifstream file1(fileName.c_str());
-	if (file1==NULL) return false;
+	if (!file1.good()) return false;
 	file1.close();
 	return true;
 }
@@ -401,7 +405,7 @@ string* searchStringInFile(const string& string2find,
 						   const string& inFileName) {
 	ifstream f;
 	f.open(inFileName.c_str());
-	if (f==NULL) {
+	if (!f.good()) {
 		string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; 
 		errorMsg::reportError(tmp);
 	}
@@ -428,7 +432,7 @@ string* searchStringInFile(const string& string2find,
 						   const string& inFileName) {// return the string that is AFTER the string to search.
 	ifstream f;
 	f.open(inFileName.c_str());
-	if (f==NULL) {
+	if (!f.good()) {
 		string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; 
 		errorMsg::reportError(tmp);
 	}
@@ -452,7 +456,7 @@ string* searchStringInFile(const string& string2find,
 bool doesWordExistInFile(const string& string2find,const string& inFileName) {
 	ifstream f;
 	f.open(inFileName.c_str());
-	if (f==NULL) {
+	if (!f.good()) {
 		string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; 
 		errorMsg::reportError(tmp);
 	}


=====================================
programs/Makefile.generic
=====================================
@@ -53,8 +53,8 @@ GENGETOPT = gengetopt
 
 .SECONDARY: $(addsuffix _cmdline.c,$(EXEC)) $(addsuffix _cmdline.h,$(EXEC)) $(addsuffix .ggo,$(EXEC))
 
-CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
-CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
+CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG 
+CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG 
 
 LDFLAGSDEBUG := $(LDFLAGS) -g 
 # sources
@@ -196,7 +196,7 @@ pl:
 	echo $(LIB)
 
 
-%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG -ftemplate-depth-25
+%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG 
 
 %.debug: %.o 
 


=====================================
programs/fastml/bbReport.cpp
=====================================
@@ -47,7 +47,7 @@ void BandBReport::makeReport() const {
 	//}
 	out<<" position is: "<<_position<<endl;
 //	cerr<<"reportFileIs: "<<_reportFileName<<endl;
-	if (out == NULL) {
+	if (!out.good()) {
 		errorMsg::reportError("unable to open output file for reporting");
 	}
 //	exit(555);


=====================================
programs/fastml/make.dep
=====================================
@@ -0,0 +1,277 @@
+fastml.o fastml.debug.o: fastml.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \
+ ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/logFile.h \
+ sequenceDataDiff.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/uniDistribution.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h bbAlg.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h bbNodeOrderAlg.h \
+ ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ bbfindBestAVDynProg.h bbReport.h ../../libs/phylogeny/distribution.h
+bbAlg.o bbAlg.debug.o: bbAlg.cpp bbAlg.h ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \
+ ../../libs/phylogeny/definitions.h bb_options.h \
+ ../../libs/phylogeny/getopt.h bb_options_list.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/gainLossAlphabet.h bbEvaluateSpecificAV.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \
+ bbReport.h ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/maseFormat.h
+bbComputeDownAlg.o bbComputeDownAlg.debug.o: bbComputeDownAlg.cpp bbComputeDownAlg.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbComputeUpAlg.o bbComputeUpAlg.debug.o: bbComputeUpAlg.cpp bbComputeUpAlg.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbEvaluateSpecificAV.o bbEvaluateSpecificAV.debug.o: bbEvaluateSpecificAV.cpp bbEvaluateSpecificAV.h \
+ bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbfindBestAVDynProg.o bbfindBestAVDynProg.debug.o: bbfindBestAVDynProg.cpp bbfindBestAVDynProg.h \
+ bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbNodeOrderAlg.o bbNodeOrderAlg.debug.o: bbNodeOrderAlg.cpp bbNodeOrderAlg.h \
+ ../../libs/phylogeny/definitions.h bb_options.h \
+ ../../libs/phylogeny/getopt.h bb_options_list.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/gainLossAlphabet.h bbComputeUpAlg.h \
+ bbComputeDownAlg.h ../../libs/phylogeny/computeMarginalAlg.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/computePijComponent.h
+bb_options.o bb_options.debug.o: bb_options.cpp bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h
+bbReport.o bbReport.debug.o: bbReport.cpp bbReport.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/amino.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/geneticCodeHolder.h ../../libs/phylogeny/codon.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/nucleotide.h ../../libs/phylogeny/codon.h
+computeMarginalReconstruction.o computeMarginalReconstruction.debug.o: computeMarginalReconstruction.cpp \
+ computeMarginalReconstruction.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/computeMarginalAlg.h ../../libs/phylogeny/treeIt.h
+jointNoGamma.o jointNoGamma.debug.o: jointNoGamma.cpp jointNoGamma.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/readTree.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h suffStatComponentJointNoGamma.h \
+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/seqContainerTreeMap.h \
+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/sequenceContainer.h
+mainbb.o mainbb.debug.o: mainbb.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \
+ ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/aaJC.h \
+ ../../libs/phylogeny/amino.h ../../libs/phylogeny/codon.h bbAlg.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \
+ ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \
+ bbReport.h ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h \
+ ../../libs/phylogeny/clustalFormat.h computeMarginalReconstruction.h \
+ ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h ../../libs/phylogeny/fastaFormat.h \
+ ../../libs/phylogeny/gammaDistribution.h jointNoGamma.h \
+ suffStatComponentJointNoGamma.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/maseFormat.h ../../libs/phylogeny/molphyFormat.h \
+ ../../libs/phylogeny/nexusFormat.h ../../libs/phylogeny/nucleotide.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/nj.h \
+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/gtrModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/hky.h \
+ ../../libs/phylogeny/phylipFormat.h ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/trivialAccelerator.h \
+ ../../libs/phylogeny/uniDistribution.h \
+ ../../libs/phylogeny/bestGtrModelParams.h \
+ ../../libs/phylogeny/gtrModel.h ../../libs/phylogeny/bestTamura92param.h \
+ ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/bestHKYparam.h \
+ ../../libs/phylogeny/hky.h ../../libs/phylogeny/bestAlphaAndK.h \
+ ../../libs/phylogeny/likelihoodComputation2Codon.h \
+ ../../libs/phylogeny/wYangModel.h ../../libs/phylogeny/bblEM2codon.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/codonUtils.h ../../libs/phylogeny/nucleotide.h \
+ ../../libs/phylogeny/amino.h ../../libs/phylogeny/fastaFormat.h \
+ ../../libs/phylogeny/clustalFormat.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h
+sequenceDataDiff.o sequenceDataDiff.debug.o: sequenceDataDiff.cpp sequenceDataDiff.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h
+suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.debug.o: suffStatComponentJointNoGamma.cpp \
+ suffStatComponentJointNoGamma.h ../../libs/phylogeny/definitions.h


=====================================
programs/gainLoss/make.dep
=====================================
@@ -0,0 +1,1014 @@
+gainLossOptions.o gainLossOptions.debug.o: gainLossOptions.cpp gainLossOptions.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/Parameters.h
+gainLoss.o gainLoss.debug.o: gainLoss.cpp computePosteriorExpectationOfChange.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/simulateJumps.h \
+ ../../libs/phylogeny/simulateJumpsAbstract.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/computeJumps.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h gainLoss.h \
+ ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h \
+ ../../libs/phylogeny/checkcovFanctors.h \
+ ../../libs/phylogeny/checkcovFanctorsWithFactors.h \
+ ../../libs/phylogeny/likelihoodComputationFactors.h \
+ ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \
+ ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \
+ ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \
+ ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \
+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \
+ optimizeGainLossModel.h ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
+ ../../libs/phylogeny/uniDistribution.h gainLossOptimizer.h \
+ ../../libs/phylogeny/gammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/simulateTree.h ../../libs/phylogeny/phylipFormat.h \
+ ../../libs/phylogeny/maseFormat.h ../../libs/phylogeny/fastaFormat.h \
+ ../../libs/phylogeny/clustalFormat.h rate4siteGL.h gainLoss4site.h \
+ siteSpecificGL.h computeCountsGL.h computeCorrelations.h \
+ ../../libs/phylogeny/Parameters.h \
+ ../../libs/phylogeny/extremeValDistribution.h simulateOnePos.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/threeStateModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \
+ ../../libs/phylogeny/oneTwoMoreModel.h sankoffReconstructGL.h bblLS.h \
+ ../../libs/phylogeny/bblEMfixRoot.h
+gainLossUtils.o gainLossUtils.debug.o: gainLossUtils.cpp gainLossUtils.h \
+ ../../libs/phylogeny/definitions.h gainLossAlphabet.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/gainLossAlphabet.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/matrixUtils.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \
+ gainLossModel.h ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/fromQtoPt.h \
+ ../../libs/phylogeny/gammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/Parameters.h
+optimizeGainLossModel.o optimizeGainLossModel.debug.o: optimizeGainLossModel.cpp \
+ optimizeGainLossModel.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/definitions.h \
+ gainLossModel.h ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/Parameters.h
+optimizeGainLossModelVV.o optimizeGainLossModelVV.debug.o: optimizeGainLossModelVV.cpp \
+ optimizeGainLossModelVV.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/definitions.h \
+ gainLossModel.h ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/Parameters.h
+likelihoodComputationGL.o likelihoodComputationGL.debug.o: \
+ ../../libs/phylogeny/likelihoodComputationGL.cpp \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/likelihoodComputation.h
+gainLossModel.o gainLossModel.debug.o: gainLossModel.cpp gainLossModel.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/fromQtoPt.h \
+ ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/errorMsg.h gainLossUtils.h gainLossAlphabet.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h
+siteSpecificGL.o siteSpecificGL.debug.o: siteSpecificGL.cpp siteSpecificGL.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/numRec.h ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h gainLossModel.h \
+ ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \
+ ../../libs/phylogeny/errorMsg.h gainLossOptions.h
+computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.debug.o: \
+ computePosteriorExpectationOfChange.cpp \
+ computePosteriorExpectationOfChange.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/simulateJumps.h \
+ ../../libs/phylogeny/simulateJumpsAbstract.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/computeJumps.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/matrixUtils.h \
+ ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/unObservableData.h gainLossOptions.h \
+ gainLossModel.h ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \
+ gainLossUtils.h gainLossAlphabet.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h
+gainLossProject.o gainLossProject.debug.o: gainLossProject.cpp gainLoss.h \
+ ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h \
+ ../../libs/phylogeny/checkcovFanctors.h \
+ ../../libs/phylogeny/checkcovFanctorsWithFactors.h \
+ ../../libs/phylogeny/likelihoodComputationFactors.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \
+ ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \
+ ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \
+ gainLossOptions.h ancestralReconstructStates.h \
+ ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \
+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \
+ optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
+ ../../libs/phylogeny/uniDistribution.h \
+ computePosteriorExpectationOfChange.h \
+ ../../libs/phylogeny/simulateJumps.h \
+ ../../libs/phylogeny/simulateJumpsAbstract.h \
+ ../../libs/phylogeny/computeJumps.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/Parameters.h
+gainLossOptimizer.o gainLossOptimizer.debug.o: gainLossOptimizer.cpp gainLossOptimizer.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/definitions.h gainLoss.h \
+ ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h \
+ ../../libs/phylogeny/checkcovFanctors.h \
+ ../../libs/phylogeny/checkcovFanctorsWithFactors.h \
+ ../../libs/phylogeny/likelihoodComputationFactors.h \
+ ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \
+ gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \
+ gainLossOptions.h ancestralReconstructStates.h \
+ ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \
+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \
+ optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
+ ../../libs/phylogeny/uniDistribution.h \
+ ../../libs/phylogeny/bblEMfixRoot.h bblLS.h
+ancestralReconstructStates.o ancestralReconstructStates.debug.o: ancestralReconstructStates.cpp \
+ ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/definitions.h gainLossAlphabet.h \
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+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \
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+rate4siteGL.o rate4siteGL.debug.o: rate4siteGL.cpp rate4siteGL.h \
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+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/definitions.h gainLoss.h \
+ ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \
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+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
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+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
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+computeCountsGL.o computeCountsGL.debug.o: computeCountsGL.cpp computeCountsGL.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/definitions.h gainLoss.h \
+ ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \
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+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
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+ ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \
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+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
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+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
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+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
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+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
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+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
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+ computePosteriorExpectationOfChange.h \
+ ../../libs/phylogeny/simulateJumps.h \
+ ../../libs/phylogeny/simulateJumpsAbstract.h \
+ ../../libs/phylogeny/computeJumps.h \
+ ../../libs/phylogeny/suffStatComponent.h
+computeCorrelations.o computeCorrelations.debug.o: computeCorrelations.cpp computeCorrelations.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/Parameters.h \
+ gainLoss.h ../../libs/phylogeny/aaJC.h \
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+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \
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+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
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+ ../../libs/phylogeny/checkcovFanctorsWithFactors.h \
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+ ../../libs/phylogeny/distanceMethod.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
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+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \
+ gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
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+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
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+ ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequence.h \
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+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h \
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+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \
+ optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
+ ../../libs/phylogeny/uniDistribution.h \
+ ../../libs/phylogeny/extremeValDistribution.h
+gainLoss4site.o gainLoss4site.debug.o: gainLoss4site.cpp gainLoss4site.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/definitions.h gainLoss.h \
+ ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \
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+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
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+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
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+ ../../libs/phylogeny/checkcovFanctorsWithFactors.h \
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+ ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \
+ gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
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+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \
+ gainLossOptions.h ancestralReconstructStates.h \
+ ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \
+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \
+ optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
+ ../../libs/phylogeny/uniDistribution.h siteSpecificGL.h
+simulateChangesAlongTree.o simulateChangesAlongTree.debug.o: simulateChangesAlongTree.cpp \
+ simulateChangesAlongTree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/matrixUtils.h \
+ gainLoss.h ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h \
+ ../../libs/phylogeny/checkcovFanctors.h \
+ ../../libs/phylogeny/checkcovFanctorsWithFactors.h \
+ ../../libs/phylogeny/likelihoodComputationFactors.h \
+ ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \
+ ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \
+ gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \
+ ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
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+ ../../libs/phylogeny/likelihoodComputation.h \
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+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \
+ optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \
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+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/siteSpecificRate.h \
+ ../../libs/phylogeny/uniDistribution.h
+simulateOnePos.o simulateOnePos.debug.o: simulateOnePos.cpp ../../libs/phylogeny/definitions.h \
+ simulateOnePos.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/readTree.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \
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+ ../../libs/phylogeny/replacementModel.h \
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+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/threeStateModel.h \
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+ ../../libs/phylogeny/oneTwoMoreModel.h \
+ ../../libs/phylogeny/simulateTree.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/threeStateAlphabet.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h \
+ ../../libs/phylogeny/uniDistribution.h ../../libs/phylogeny/sequence.h \
+ simulateChangesAlongTree.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/fastaFormat.h gainLoss.h \
+ ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
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+ ../../libs/phylogeny/checkcovFanctors.h \
+ ../../libs/phylogeny/checkcovFanctorsWithFactors.h \
+ ../../libs/phylogeny/likelihoodComputationFactors.h \
+ ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/fastStartTree.h \
+ gainLossAlphabet.h gainLossModel.h \
+ ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \
+ ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h gainLossOptions.h \
+ ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \
+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \
+ optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/talRandom.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/siteSpecificRate.h
+bblLS.o bblLS.debug.o: bblLS.cpp bblLS.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h gainLossUtils.h \
+ gainLossAlphabet.h ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/matrixUtils.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/likelihoodComputationGL.h \
+ ../../libs/phylogeny/computeUpAlg.h gainLossOptions.h
+sankoffReconstructGL.o sankoffReconstructGL.debug.o: sankoffReconstructGL.cpp sankoffReconstructGL.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/gainLossAlphabet.h gainLossUtils.h \
+ gainLossAlphabet.h ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/gammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \
+ ../../libs/phylogeny/GamMixtureOptimizer.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/mixtureDistribution.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \
+ ../../libs/phylogeny/distributionPlusInvariant.h \
+ ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/matrixUtils.h \
+ ../../libs/phylogeny/mixtureDistribution.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h \
+ ../../libs/phylogeny/trivialAccelerator.h \
+ ../../libs/phylogeny/threeStateAlphabet.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/treeUtil.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/geneticCodeHolder.h ../../libs/phylogeny/codon.h \
+ ../../libs/phylogeny/nucleotide.h ../../libs/phylogeny/integerAlphabet.h \
+ gainLossOptions.h


=====================================
programs/indelCoder/make.dep
=====================================
@@ -0,0 +1,51 @@
+indelCoder.o indelCoder.debug.o: indelCoder.cpp indelCoder.h gaps.h \
+ ../../libs/phylogeny/definitions.h character.h \
+ ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \
+ indelCoderOptions.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/talRandom.h indelCoderUtils.h
+indelCoderOptions.o indelCoderOptions.debug.o: indelCoderOptions.cpp indelCoderOptions.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/Parameters.h
+indelCoderProject.o indelCoderProject.debug.o: indelCoderProject.cpp indelCoder.h gaps.h \
+ ../../libs/phylogeny/definitions.h character.h \
+ ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \
+ indelCoderOptions.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/talRandom.h indelCoderUtils.h \
+ ../../libs/phylogeny/Parameters.h
+indelCoderUtils.o indelCoderUtils.debug.o: indelCoderUtils.cpp indelCoderUtils.h \
+ ../../libs/phylogeny/logFile.h indelCoder.h gaps.h \
+ ../../libs/phylogeny/definitions.h character.h \
+ ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \
+ indelCoderOptions.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/talRandom.h
+character.o character.debug.o: character.cpp character.h ../../libs/phylogeny/definitions.h \
+ gaps.h ../../libs/phylogeny/matrixUtils.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/errorMsg.h indelCoderOptions.h
+gaps.o gaps.debug.o: gaps.cpp gaps.h ../../libs/phylogeny/definitions.h



View it on GitLab: https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad

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