Update upstream source from tag 'upstream/3.11'
Update to upstream version '3.11'
with Debian dir 79e1638c1bce5be9abfac932fc8c543ed8b92fe0
Andreas Tille
4 years ago
| 0 | #! /usr/local/bin/gmake | |
| 1 | # $Id: Makefile 11759 2013-09-24 13:45:40Z elilevy $ | |
| 2 | # makfile for yaep5 | |
| 3 | ||
| 4 | ||
| 5 | ||
| 6 | # use LOGREP=t or DOUBLEREP=t to activate logRep or doubleRep respectively (or setenv DOUBLEREP in the shell) | |
| 7 | #DOUBLEREP=t | |
| 8 | #LOGREP=t | |
| 9 | ||
| 10 | ||
| 11 | Libsources= AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp \ | |
| 12 | allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp \ | |
| 13 | bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp \ | |
| 14 | bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp \ | |
| 15 | chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp \ | |
| 16 | computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp \ | |
| 17 | computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp \ | |
| 18 | computeSubstitutionCounts.cpp \ | |
| 19 | computePosteriorExpectationOfSubstitutions.cpp \ | |
| 20 | computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp \ | |
| 21 | ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp \ | |
| 22 | distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp \ | |
| 23 | fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp \ | |
| 24 | fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp \ | |
| 25 | fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp \ | |
| 26 | generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp \ | |
| 27 | generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp \ | |
| 28 | granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp \ | |
| 29 | likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp \ | |
| 30 | likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp \ | |
| 31 | molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp \ | |
| 32 | nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp \ | |
| 33 | pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp \ | |
| 34 | replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp \ | |
| 35 | sequence.cpp sequenceContainer.cpp simulateTree.cpp \ | |
| 36 | siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp \ | |
| 37 | splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp \ | |
| 38 | talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp \ | |
| 39 | uniformDistribution.cpp cmdline2EvolObjs.cpp \ | |
| 40 | generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp \ | |
| 41 | givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp \ | |
| 42 | posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp \ | |
| 43 | logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp \ | |
| 44 | replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp \ | |
| 45 | C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp \ | |
| 46 | betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp \ | |
| 47 | samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp \ | |
| 48 | likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp \ | |
| 49 | fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp \ | |
| 50 | tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp \ | |
| 51 | simulateCodonsJumps.cpp \ | |
| 52 | simulateJumpsAbstract.cpp \ | |
| 53 | ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp\ | |
| 54 | extremeValDistribution.cpp \ | |
| 55 | gammaDistributionFixedCategories.cpp generalGammaDistributionPlusInvariant.cpp gammaDistributionPlusInvariant.cpp \ | |
| 56 | distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp \ | |
| 57 | optGammaMixtureLS.cpp mixtureDistribution.cpp suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp \ | |
| 58 | wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp \ | |
| 59 | threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp \ | |
| 60 | bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp\ | |
| 61 | gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp | |
| 62 | ||
| 63 | # do not use: fromInstructionFile.cpp, simulateSequnce.cpp split.save.cpp | |
| 64 | ||
| 65 | ||
| 66 | # LibCsources= cmdline.c | |
| 67 | # LibCsources += getopt.c getopt1.c | |
| 68 | ||
| 69 | EXEC = | |
| 70 | #TEST_EXEC_SUB = split_test splitMap_test bootstrap_test | |
| 71 | TEST_EXEC = $(addprefix tests/,$(TEST_EXEC_SUB)) | |
| 72 | LIB = libEvolTree.a | |
| 73 | DEBUGLIB = $(LIB:.a=Debug.a) | |
| 74 | DOUBLEREPLIB = $(LIB:.a=DoubleRep.a) | |
| 75 | ||
| 76 | ||
| 77 | #CC=g++ | |
| 78 | CXX=g++ | |
| 79 | CC=$(CXX) | |
| 80 | ||
| 81 | #requres 2.13, but may work with 2.11 | |
| 82 | GENGETOPT = gengetopt | |
| 83 | # osX/tiger | |
| 84 | #GENGETOPT = /opt/local/bin/gengetopt | |
| 85 | ||
| 86 | .SECONDARY: semphy_cmdline.c semphy_cmdline.h | |
| 87 | ||
| 88 | #LDFLAGS= | |
| 89 | ||
| 90 | CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32AGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -DVERBOS | |
| 91 | #CPPFLAGSDOU= $(CPPFLAGS) | |
| 92 | #-pg | |
| 93 | ||
| 94 | ||
| 95 | #CPPFLAGS+= -I/usr/include/g++-v3 | |
| 96 | #CPPFLAGS+= -DLOG -DLOGCLS -DMEMCHK | |
| 97 | ||
| 98 | # sources | |
| 99 | sources= $(Libsources) $(LibCsources) $(addsuffix .cpp,$(EXEC) $(TEST_EXEC)) | |
| 100 | ||
| 101 | .PHONY: tests lib test debug %.debug | |
| 102 | .PHONY: dat DOUBLEREP doubleRep | |
| 103 | ||
| 104 | all: lib $(EXEC) | |
| 105 | ||
| 106 | test: all tests | |
| 107 | +cd tests; make -k test | |
| 108 | ||
| 109 | #ifdef DOUBLEREP | |
| 110 | #CPPFLAGS+= -DLOGREP | |
| 111 | #CPPFLAGSDEBUG += -DLOGREP | |
| 112 | #LDFLAGSDEBUG += -DLOGREP | |
| 113 | #endif | |
| 114 | ||
| 115 | ifdef DOUBLEREP | |
| 116 | CPPFLAGS+= -DDOUBLEREP | |
| 117 | CPPFLAGSDEBUG += -DDOUBLEREP | |
| 118 | LDFLAGSDEBUG += -DDOUBLEREP | |
| 119 | endif | |
| 120 | ||
| 121 | debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 | |
| 122 | debug: $(DEBUGLIB) | |
| 123 | pl: | |
| 124 | @echo "lib ="$(LIB) | |
| 125 | @echo "debug="$(DEBUGLIB) | |
| 126 | #debug: all | |
| 127 | # cp libEvolTree.a libEvolTreeDebug.a | |
| 128 | ||
| 129 | # <<<<<<< Makefile | |
| 130 | # %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25 | |
| 131 | # % debug: LIB = libEvolTreeDebug.a | |
| 132 | # %.debug: % | |
| 133 | # @echo "made \""$(*)"\" in debug mode" | |
| 134 | ||
| 135 | # ======= | |
| 136 | #>>>>>>> 2.34 | |
| 137 | ||
| 138 | lib: $(LIB) | |
| 139 | ||
| 140 | $(LIB): $(Libsources:.cpp=.o) $(LibCsources:.c=.o) | |
| 141 | ar rv $@ $? | |
| 142 | ranlib $@ | |
| 143 | ||
| 144 | tags: *.cpp *.h | |
| 145 | etags --members --language=c++ $^ | |
| 146 | ||
| 147 | $(EXEC) $(TEST_EXEC): $(LIB) | |
| 148 | tests: $(TEST_EXEC) | |
| 149 | ||
| 150 | -include make.dep | |
| 151 | ||
| 152 | install: | |
| 153 | cd ../fast; make -f Makefile.lib install_do | |
| 154 | ||
| 155 | ||
| 156 | clean: | |
| 157 | -rm -f $(LIB) $(DEBUGLIB) $(DOUBLEREPLIB) $(EXEC) $(TEST_EXEC) *.o | |
| 158 | ||
| 159 | ||
| 160 | ifneq ($(wildcard make.dep), make.dep) | |
| 161 | make.dep: depend | |
| 162 | endif | |
| 163 | ||
| 164 | depend makedep: _make.dep | |
| 165 | @mv -f _make.dep make.dep | |
| 166 | ||
| 167 | _make.dep: $(sources) | |
| 168 | @echo making depend | |
| 169 | # $(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@ ; [ -s $@ ] || rm -f $@' | |
| 170 | @$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed "s/\(^[^.]*\)\.o/\1.o \1.debug.o/g" > $@' | |
| 171 | _fast: | |
| 172 | cd ../fast;make -f Makefile.lib -k all | |
| 173 | ||
| 174 | fast.% _fast.%: | |
| 175 | cd ../fast;make -f Makefile.lib -k $(*) | |
| 176 | ||
| 177 | ||
| 178 | simulateSequnce: simulateSequnce_cmdline.o | |
| 179 | ||
| 180 | ||
| 181 | evolObjsTest.ggo: evolObjs.header evolObjs.args | |
| 182 | cat $^ > $@ | |
| 183 | ||
| 184 | ||
| 185 | # commandline (gengetopts) | |
| 186 | %_cmdline.h %_cmdline.c: %.ggo | |
| 187 | $(GENGETOPT) -i$< -F$(*)_cmdline | |
| 188 | ||
| 189 | %.dat.q: %.dat | |
| 190 | awk 'BEGIN{RS="[\n\r]+";};{print "\" "$$0" \"\r"}' $< > $@ | |
| 191 | # cat $@ | |
| 192 | ||
| 193 | DAT = cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q | |
| 194 | ||
| 195 | dat: $(DAT) | |
| 196 | ||
| 197 | cleandat: | |
| 198 | rm $(DAT) | |
| 199 | ||
| 200 | datMatrixHolder.o: $(DAT) | |
| 201 | ||
| 202 | .PRECIOUS: $(DAT) | |
| 203 | ||
| 204 | debug: LIB = $(DEBUGLIB) | |
| 205 | ||
| 206 | %.debug: CPPFLAGS = $(CPPFLAGSDEBUG) | |
| 207 | %.debug: % | |
| 208 | @echo "made \""$(*)"\" in debug mode" | |
| 209 | ||
| 210 | ||
| 211 | %.debug.o: %.c | |
| 212 | $(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@ | |
| 213 | ||
| 214 | %.debug.o: %.cpp | |
| 215 | $(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@ | |
| 216 | ||
| 217 | $(DEBUGLIB): $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o) | |
| 218 | ar rv $@ $? | |
| 219 | ranlib $@ | |
| 220 | ||
| 221 | #doubleRep: LOGREP=t | |
| 222 | #doubleRep: CPPFLAGS+= -DLOGREP | |
| 223 | doubleRep: DOUBLEREP=t | |
| 224 | doubleRep: CPPFLAGS+= -DDOUBLEREP | |
| 225 | doubleRep: $(DOUBLEREPLIB) | |
| 226 | ||
| 227 | %.doubleRep.o: %.c | |
| 228 | $(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@ | |
| 229 | ||
| 230 | %.doubleRep.o: %.cpp | |
| 231 | $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@ | |
| 232 | ||
| 233 | $(DOUBLEREPLIB): $(Libsources:.cpp=.doubleRep.o) $(LibCsources:.c=.doubleRep.o) | |
| 234 | ar rv $@ $? | |
| 235 | ranlib $@ | |
| 236 | ||
| 237 | # DO NOT DELETE |
| 87 | 87 | |
| 88 | 88 | #LDFLAGS= |
| 89 | 89 | |
| 90 | CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 | |
| 91 | CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -DVERBOS | |
| 90 | CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -DLOG | |
| 91 | CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -DVERBOS | |
| 92 | 92 | #CPPFLAGSDOU= $(CPPFLAGS) |
| 93 | 93 | #-pg |
| 94 | 94 | |
| 119 | 119 | LDFLAGSDEBUG += -DDOUBLEREP |
| 120 | 120 | endif |
| 121 | 121 | |
| 122 | debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 | |
| 122 | debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG | |
| 123 | 123 | debug: $(DEBUGLIB) |
| 124 | 124 | pl: |
| 125 | 125 | @echo "lib ="$(LIB) |
| 128 | 128 | # cp libEvolTree.a libEvolTreeDebug.a |
| 129 | 129 | |
| 130 | 130 | # <<<<<<< Makefile |
| 131 | # %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25 | |
| 131 | # %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG | |
| 132 | 132 | # % debug: LIB = libEvolTreeDebug.a |
| 133 | 133 | # %.debug: % |
| 134 | 134 | # @echo "made \""$(*)"\" in debug mode" |
| 0 | // $Id: errorMsg.cpp 6066 2009-04-14 19:11:10Z itaymay $ | |
| 0 | // $Id: errorMsg.cpp 15479 2016-10-10 16:25:21Z elilevy $ | |
| 1 | 1 | |
| 2 | 2 | // version 1.01 |
| 3 | 3 | // last modified 1 Jan 2004 |
| 15 | 15 | for (int i =0 ; i < textToPrint.size() ; ++i) { |
| 16 | 16 | LOG(1,<<textToPrint[i]<<endl); |
| 17 | 17 | cerr<<textToPrint[i]<<endl; |
| 18 | if (_errorOut != NULL && *_errorOut != cerr) { | |
| 18 | if (_errorOut != NULL && _errorOut != &cerr) { | |
| 19 | 19 | (*_errorOut)<<textToPrint[i]<<endl; |
| 20 | 20 | } |
| 21 | 21 | } |
| 30 | 30 | void errorMsg::reportError(const string& textToPrint, const int exitCode) { |
| 31 | 31 | LOG(1,<<endl<<textToPrint<<endl); |
| 32 | 32 | cerr<<endl<<textToPrint<<endl; |
| 33 | if (_errorOut != NULL && *_errorOut != cerr) { | |
| 33 | if (_errorOut != NULL && _errorOut != &cerr) { | |
| 34 | 34 | (*_errorOut)<<textToPrint<<endl; |
| 35 | 35 | } |
| 36 | 36 | if (errno!=0){ |
| 0 | AddLog.o AddLog.debug.o: AddLog.cpp AddLog.h | |
| 1 | NNiProp.o NNiProp.debug.o: NNiProp.cpp definitions.h treeIt.h errorMsg.h tree.h \ | |
| 2 | readTree.h logFile.h treeUtil.h NNiProp.h sequenceContainer.h sequence.h \ | |
| 3 | alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 4 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 5 | bblEM.h countTableComponent.h computePijComponent.h \ | |
| 6 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 7 | generalGammaDistribution.h suffStatComponent.h unObservableData.h \ | |
| 8 | bblEMProportional.h | |
| 9 | NNiSep.o NNiSep.debug.o: NNiSep.cpp definitions.h treeIt.h errorMsg.h tree.h readTree.h \ | |
| 10 | logFile.h treeUtil.h NNiSep.h sequenceContainer.h sequence.h alphabet.h \ | |
| 11 | mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \ | |
| 12 | pijAccelerator.h replacementModel.h distribution.h bblEM.h \ | |
| 13 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 14 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 15 | unObservableData.h bblEMSeperate.h | |
| 16 | Nni.o Nni.debug.o: Nni.cpp definitions.h treeUtil.h tree.h readTree.h errorMsg.h \ | |
| 17 | logFile.h treeIt.h Nni.h sequenceContainer.h sequence.h alphabet.h \ | |
| 18 | mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \ | |
| 19 | pijAccelerator.h replacementModel.h distribution.h bblEM.h \ | |
| 20 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 21 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 22 | unObservableData.h | |
| 23 | aaJC.o aaJC.debug.o: aaJC.cpp aaJC.h replacementModel.h definitions.h errorMsg.h | |
| 24 | allTrees.o allTrees.debug.o: allTrees.cpp definitions.h allTrees.h tree.h readTree.h \ | |
| 25 | errorMsg.h logFile.h sequenceContainer.h sequence.h alphabet.h \ | |
| 26 | mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \ | |
| 27 | pijAccelerator.h replacementModel.h distribution.h treeUtil.h treeIt.h \ | |
| 28 | bblEM.h countTableComponent.h computePijComponent.h \ | |
| 29 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 30 | generalGammaDistribution.h suffStatComponent.h unObservableData.h | |
| 31 | allTreesSeparateModel.o allTreesSeparateModel.debug.o: allTreesSeparateModel.cpp definitions.h treeIt.h \ | |
| 32 | errorMsg.h tree.h readTree.h logFile.h allTreesSeparateModel.h \ | |
| 33 | sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 34 | gainLossAlphabet.h stochasticProcess.h pijAccelerator.h \ | |
| 35 | replacementModel.h distribution.h bblEMSeperate.h | |
| 36 | alphabet.o alphabet.debug.o: alphabet.cpp alphabet.h | |
| 37 | amino.o amino.debug.o: amino.cpp amino.h definitions.h errorMsg.h alphabet.h \ | |
| 38 | geneticCodeHolder.h codon.h someUtil.h logFile.h | |
| 39 | bestAlpha.o bestAlpha.debug.o: bestAlpha.cpp bestAlpha.h definitions.h \ | |
| 40 | likelihoodComputation.h computePijComponent.h tree.h readTree.h \ | |
| 41 | errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 42 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 43 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 44 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 45 | suffStatComponent.h unObservableData.h bblEM.h countTableComponent.h \ | |
| 46 | bblEMProportionalEB.h bblLSProportionalEB.h numRec.h \ | |
| 47 | uniformDistribution.h | |
| 48 | bestAlphaManyTrees.o bestAlphaManyTrees.debug.o: bestAlphaManyTrees.cpp bestAlphaManyTrees.h \ | |
| 49 | definitions.h computePijComponent.h tree.h readTree.h errorMsg.h \ | |
| 50 | logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 51 | distribution.h multipleStochasticProcess.h gammaDistribution.h \ | |
| 52 | generalGammaDistribution.h sequenceContainer.h sequence.h alphabet.h \ | |
| 53 | mulAlphabet.h someUtil.h gainLossAlphabet.h bblEM.h \ | |
| 54 | countTableComponent.h suffStatComponent.h unObservableData.h \ | |
| 55 | likelihoodComputation.h bestAlpha.h numRec.h uniformDistribution.h \ | |
| 56 | bblEMProportional.h bblEMSeperate.h | |
| 57 | bestHKYparam.o bestHKYparam.debug.o: bestHKYparam.cpp bestHKYparam.h definitions.h \ | |
| 58 | likelihoodComputation.h computePijComponent.h tree.h readTree.h \ | |
| 59 | errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 60 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 61 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 62 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 63 | suffStatComponent.h unObservableData.h hky.h bblEM.h \ | |
| 64 | countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \ | |
| 65 | numRec.h uniformDistribution.h bestAlpha.h | |
| 66 | bootstrap.o bootstrap.debug.o: bootstrap.cpp definitions.h someUtil.h logFile.h alphabet.h \ | |
| 67 | bootstrap.h split.h splitMap.h tree.h readTree.h errorMsg.h treeUtil.h \ | |
| 68 | splitTreeUtil.h | |
| 69 | bblEM.o bblEM.debug.o: bblEM.cpp bblEM.h definitions.h tree.h readTree.h errorMsg.h \ | |
| 70 | logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 71 | distribution.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h \ | |
| 72 | someUtil.h gainLossAlphabet.h countTableComponent.h \ | |
| 73 | computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \ | |
| 74 | generalGammaDistribution.h suffStatComponent.h unObservableData.h \ | |
| 75 | likelihoodComputation.h computeUpAlg.h computeDownAlg.h computeCounts.h \ | |
| 76 | treeIt.h fromCountTableComponentToDistance.h | |
| 77 | bblEMfixRoot.o bblEMfixRoot.debug.o: bblEMfixRoot.cpp bblEMfixRoot.h definitions.h tree.h \ | |
| 78 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 79 | replacementModel.h distribution.h sequenceContainer.h sequence.h \ | |
| 80 | alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 81 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 82 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 83 | unObservableData.h likelihoodComputation.h computeUpAlg.h \ | |
| 84 | computeDownAlg.h computeCounts.h treeIt.h \ | |
| 85 | fromCountTableComponentToDistancefixRoot.h | |
| 86 | bblEMProprtional.o bblEMProprtional.debug.o: bblEMProprtional.cpp bblEM.h definitions.h tree.h \ | |
| 87 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 88 | replacementModel.h distribution.h sequenceContainer.h sequence.h \ | |
| 89 | alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 90 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 91 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 92 | unObservableData.h bblEMProportional.h likelihoodComputation.h \ | |
| 93 | computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \ | |
| 94 | fromCountTableComponentToDistance.h \ | |
| 95 | fromCountTableComponentToDistanceProp.h | |
| 96 | bblEMProportionalEB.o bblEMProportionalEB.debug.o: bblEMProportionalEB.cpp bblEM.h definitions.h \ | |
| 97 | tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \ | |
| 98 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 99 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 100 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 101 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 102 | unObservableData.h bblEMProportionalEB.h likelihoodComputation.h \ | |
| 103 | computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \ | |
| 104 | fromCountTableComponentToDistance.h \ | |
| 105 | fromCountTableComponentToDistancePropEB.h | |
| 106 | bblLSProportionalEB.o bblLSProportionalEB.debug.o: bblLSProportionalEB.cpp bblLSProportionalEB.h \ | |
| 107 | definitions.h tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \ | |
| 108 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 109 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 110 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 111 | generalGammaDistribution.h likelihoodComputation.h computePijComponent.h \ | |
| 112 | suffStatComponent.h unObservableData.h numRec.h uniformDistribution.h | |
| 113 | bblEMSeperate.o bblEMSeperate.debug.o: bblEMSeperate.cpp bblEM.h definitions.h tree.h \ | |
| 114 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 115 | replacementModel.h distribution.h sequenceContainer.h sequence.h \ | |
| 116 | alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 117 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 118 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 119 | unObservableData.h bblEMSeperate.h | |
| 120 | chebyshevAccelerator.o chebyshevAccelerator.debug.o: chebyshevAccelerator.cpp chebyshevAccelerator.h \ | |
| 121 | pijAccelerator.h definitions.h replacementModel.h | |
| 122 | clustalFormat.o clustalFormat.debug.o: clustalFormat.cpp clustalFormat.h sequenceContainer.h \ | |
| 123 | definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 124 | logFile.h gainLossAlphabet.h codon.h geneticCodeHolder.h | |
| 125 | codon.o codon.debug.o: codon.cpp codon.h definitions.h errorMsg.h someUtil.h logFile.h \ | |
| 126 | alphabet.h geneticCodeHolder.h nucleotide.h amino.h matrixUtils.h \ | |
| 127 | sequenceContainer.h sequence.h mulAlphabet.h gainLossAlphabet.h | |
| 128 | codonJC.o codonJC.debug.o: codonJC.cpp codonJC.h replacementModel.h definitions.h | |
| 129 | computeCounts.o computeCounts.debug.o: computeCounts.cpp computeCounts.h definitions.h \ | |
| 130 | countTableComponent.h sequenceContainer.h sequence.h errorMsg.h \ | |
| 131 | alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h \ | |
| 132 | computePijComponent.h tree.h readTree.h stochasticProcess.h \ | |
| 133 | pijAccelerator.h replacementModel.h distribution.h \ | |
| 134 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 135 | generalGammaDistribution.h suffStatComponent.h | |
| 136 | computeDownAlg.o computeDownAlg.debug.o: computeDownAlg.cpp definitions.h computeDownAlg.h \ | |
| 137 | tree.h readTree.h errorMsg.h logFile.h suffStatComponent.h \ | |
| 138 | sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 139 | gainLossAlphabet.h computePijComponent.h stochasticProcess.h \ | |
| 140 | pijAccelerator.h replacementModel.h distribution.h \ | |
| 141 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 142 | generalGammaDistribution.h treeIt.h | |
| 143 | computeMarginalAlg.o computeMarginalAlg.debug.o: computeMarginalAlg.cpp definitions.h treeIt.h \ | |
| 144 | errorMsg.h tree.h readTree.h logFile.h computeMarginalAlg.h \ | |
| 145 | suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \ | |
| 146 | mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \ | |
| 147 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 148 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 149 | generalGammaDistribution.h | |
| 150 | computePijComponent.o computePijComponent.debug.o: computePijComponent.cpp definitions.h treeIt.h \ | |
| 151 | errorMsg.h tree.h readTree.h logFile.h computePijComponent.h \ | |
| 152 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 153 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 154 | generalGammaDistribution.h | |
| 155 | computeUpAlg.o computeUpAlg.debug.o: computeUpAlg.cpp definitions.h computeUpAlg.h tree.h \ | |
| 156 | readTree.h errorMsg.h logFile.h suffStatComponent.h sequenceContainer.h \ | |
| 157 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 158 | computePijComponent.h stochasticProcess.h pijAccelerator.h \ | |
| 159 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 160 | gammaDistribution.h generalGammaDistribution.h treeIt.h \ | |
| 161 | seqContainerTreeMap.h | |
| 162 | computeUpAlgFactors.o computeUpAlgFactors.debug.o: computeUpAlgFactors.cpp definitions.h \ | |
| 163 | computeUpAlg.h tree.h readTree.h errorMsg.h logFile.h \ | |
| 164 | suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \ | |
| 165 | mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \ | |
| 166 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 167 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 168 | generalGammaDistribution.h seqContainerTreeMap.h treeIt.h | |
| 169 | computeSubstitutionCounts.o computeSubstitutionCounts.debug.o: computeSubstitutionCounts.cpp \ | |
| 170 | computeSubstitutionCounts.h definitions.h replacementModel.h \ | |
| 171 | sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 172 | someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \ | |
| 173 | computePosteriorExpectationOfSubstitutions.h simulateJumps.h \ | |
| 174 | simulateJumpsAbstract.h stochasticProcess.h pijAccelerator.h \ | |
| 175 | distribution.h suffStatComponent.h computePijComponent.h \ | |
| 176 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 177 | generalGammaDistribution.h \ | |
| 178 | computePosteriorExpectationOfSubstitutions_nonReversibleSp.h \ | |
| 179 | matrixUtils.h simulateCodonsJumps.h codon.h geneticCodeHolder.h treeIt.h \ | |
| 180 | treeUtil.h | |
| 181 | computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.debug.o: \ | |
| 182 | computePosteriorExpectationOfSubstitutions.cpp \ | |
| 183 | computePosteriorExpectationOfSubstitutions.h definitions.h \ | |
| 184 | simulateJumps.h simulateJumpsAbstract.h tree.h readTree.h errorMsg.h \ | |
| 185 | logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 186 | distribution.h alphabet.h sequenceContainer.h sequence.h mulAlphabet.h \ | |
| 187 | someUtil.h gainLossAlphabet.h suffStatComponent.h computePijComponent.h \ | |
| 188 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 189 | generalGammaDistribution.h computeDownAlg.h computeUpAlg.h matrixUtils.h \ | |
| 190 | treeIt.h likelihoodComputation.h unObservableData.h | |
| 191 | computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.debug.o: \ | |
| 192 | computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp \ | |
| 193 | definitions.h computeDownAlg.h tree.h readTree.h errorMsg.h logFile.h \ | |
| 194 | suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \ | |
| 195 | mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \ | |
| 196 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 197 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 198 | generalGammaDistribution.h computeUpAlg.h matrixUtils.h treeIt.h \ | |
| 199 | likelihoodComputation.h unObservableData.h \ | |
| 200 | computePosteriorExpectationOfSubstitutions_nonReversibleSp.h \ | |
| 201 | computePosteriorExpectationOfSubstitutions.h simulateJumps.h \ | |
| 202 | simulateJumpsAbstract.h | |
| 203 | ConversionUtils.o ConversionUtils.debug.o: ConversionUtils.cpp ConversionUtils.h definitions.h \ | |
| 204 | someUtil.h logFile.h alphabet.h errorMsg.h | |
| 205 | countTableComponent.o countTableComponent.debug.o: countTableComponent.cpp countTableComponent.h \ | |
| 206 | definitions.h logFile.h | |
| 207 | datMatrixHolder.o datMatrixHolder.debug.o: datMatrixHolder.cpp datMatrixHolder.h cpREV45.dat.q \ | |
| 208 | dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q \ | |
| 209 | adrianCodon.dat.q LG.dat.q | |
| 210 | distanceTable.o distanceTable.debug.o: distanceTable.cpp definitions.h distanceTable.h \ | |
| 211 | distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 212 | someUtil.h logFile.h sequenceContainer.h gainLossAlphabet.h | |
| 213 | distribution.o distribution.debug.o: distribution.cpp distribution.h definitions.h errorMsg.h | |
| 214 | errorMsg.o errorMsg.debug.o: errorMsg.cpp definitions.h errorMsg.h logFile.h | |
| 215 | evaluateCharacterFreq.o evaluateCharacterFreq.debug.o: evaluateCharacterFreq.cpp \ | |
| 216 | evaluateCharacterFreq.h sequenceContainer.h definitions.h sequence.h \ | |
| 217 | errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 218 | gainLossAlphabet.h | |
| 219 | fastStartTree.o fastStartTree.debug.o: fastStartTree.cpp definitions.h tree.h readTree.h \ | |
| 220 | errorMsg.h logFile.h treeUtil.h fastStartTree.h stochasticProcess.h \ | |
| 221 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 222 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 223 | bblEM.h countTableComponent.h computePijComponent.h \ | |
| 224 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 225 | generalGammaDistribution.h suffStatComponent.h unObservableData.h \ | |
| 226 | likeDist.h distanceMethod.h jcDistance.h likelihoodComputation.h \ | |
| 227 | getRandomWeights.h distanceTable.h nj.h njConstrain.h distances2Tree.h | |
| 228 | fastaFormat.o fastaFormat.debug.o: fastaFormat.cpp fastaFormat.h sequenceContainer.h \ | |
| 229 | definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 230 | logFile.h gainLossAlphabet.h ConversionUtils.h | |
| 231 | findRateOfGene.o findRateOfGene.debug.o: findRateOfGene.cpp definitions.h findRateOfGene.h \ | |
| 232 | numRec.h errorMsg.h uniformDistribution.h distribution.h logFile.h \ | |
| 233 | likelihoodComputation.h computePijComponent.h tree.h readTree.h \ | |
| 234 | stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 235 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 236 | generalGammaDistribution.h sequenceContainer.h sequence.h alphabet.h \ | |
| 237 | mulAlphabet.h someUtil.h gainLossAlphabet.h suffStatComponent.h \ | |
| 238 | unObservableData.h computeUpAlg.h | |
| 239 | fromCountTableComponentToDistance.o fromCountTableComponentToDistance.debug.o: \ | |
| 240 | fromCountTableComponentToDistance.cpp \ | |
| 241 | fromCountTableComponentToDistance.h definitions.h countTableComponent.h \ | |
| 242 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 243 | unObservableData.h tree.h readTree.h errorMsg.h logFile.h \ | |
| 244 | sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 245 | gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \ | |
| 246 | gammaDistribution.h generalGammaDistribution.h likeDist.h \ | |
| 247 | distanceMethod.h jcDistance.h | |
| 248 | fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.debug.o: \ | |
| 249 | fromCountTableComponentToDistancefixRoot.cpp \ | |
| 250 | fromCountTableComponentToDistancefixRoot.h definitions.h \ | |
| 251 | countTableComponent.h stochasticProcess.h pijAccelerator.h \ | |
| 252 | replacementModel.h distribution.h unObservableData.h tree.h readTree.h \ | |
| 253 | errorMsg.h logFile.h sequenceContainer.h sequence.h alphabet.h \ | |
| 254 | mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \ | |
| 255 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 256 | generalGammaDistribution.h likeDistfixRoot.h distanceMethod.h \ | |
| 257 | jcDistance.h | |
| 258 | fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.debug.o: \ | |
| 259 | fromCountTableComponentToDistanceProp.cpp \ | |
| 260 | fromCountTableComponentToDistanceProp.h definitions.h \ | |
| 261 | countTableComponent.h stochasticProcess.h pijAccelerator.h \ | |
| 262 | replacementModel.h distribution.h likeDistProp.h | |
| 263 | fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.debug.o: \ | |
| 264 | fromCountTableComponentToDistancePropEB.cpp \ | |
| 265 | fromCountTableComponentToDistancePropEB.h definitions.h \ | |
| 266 | countTableComponent.h multipleStochasticProcess.h stochasticProcess.h \ | |
| 267 | pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \ | |
| 268 | generalGammaDistribution.h errorMsg.h likeDistPropEB.h logFile.h | |
| 269 | fromQtoPt.o fromQtoPt.debug.o: fromQtoPt.cpp definitions.h fromQtoPt.h replacementModel.h \ | |
| 270 | errorMsg.h numRec.h uniformDistribution.h distribution.h logFile.h \ | |
| 271 | matrixUtils.h | |
| 272 | generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.debug.o: \ | |
| 273 | generalGammaDistributionFixedCategories.cpp \ | |
| 274 | generalGammaDistributionFixedCategories.h definitions.h \ | |
| 275 | generalGammaDistribution.h distribution.h errorMsg.h gammaUtilities.h \ | |
| 276 | numRec.h uniformDistribution.h logFile.h | |
| 277 | gammaDistribution.o gammaDistribution.debug.o: gammaDistribution.cpp definitions.h \ | |
| 278 | gammaDistribution.h generalGammaDistribution.h distribution.h errorMsg.h \ | |
| 279 | gammaUtilities.h numRec.h uniformDistribution.h logFile.h | |
| 280 | gammaUtilities.o gammaUtilities.debug.o: gammaUtilities.cpp gammaUtilities.h definitions.h \ | |
| 281 | numRec.h errorMsg.h uniformDistribution.h distribution.h logFile.h | |
| 282 | generalGammaDistribution.o generalGammaDistribution.debug.o: generalGammaDistribution.cpp \ | |
| 283 | generalGammaDistribution.h definitions.h distribution.h gammaUtilities.h \ | |
| 284 | numRec.h errorMsg.h uniformDistribution.h logFile.h | |
| 285 | getRandomWeights.o getRandomWeights.debug.o: getRandomWeights.cpp getRandomWeights.h definitions.h \ | |
| 286 | talRandom.h logFile.h | |
| 287 | goldmanYangModel.o goldmanYangModel.debug.o: goldmanYangModel.cpp goldmanYangModel.h definitions.h \ | |
| 288 | replacementModel.h fromQtoPt.h granthamChemicalDistances.h codon.h \ | |
| 289 | errorMsg.h someUtil.h logFile.h alphabet.h geneticCodeHolder.h \ | |
| 290 | readDatMatrix.h datMatrixHolder.h | |
| 291 | granthamChemicalDistances.o granthamChemicalDistances.debug.o: granthamChemicalDistances.cpp \ | |
| 292 | granthamChemicalDistances.h definitions.h | |
| 293 | hky.o hky.debug.o: hky.cpp hky.h replacementModel.h definitions.h errorMsg.h | |
| 294 | simulateWithDependence.o simulateWithDependence.debug.o: simulateWithDependence.cpp \ | |
| 295 | simulateWithDependence.h tree.h definitions.h readTree.h errorMsg.h \ | |
| 296 | logFile.h alphabet.h nucleotide.h simulateTree.h stochasticProcess.h \ | |
| 297 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 298 | sequence.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 299 | trivialAccelerator.h uniDistribution.h \ | |
| 300 | generalGammaDistributionPlusInvariant.h distributionPlusInvariant.h \ | |
| 301 | generalGammaDistribution.h gammaUtilities.h numRec.h \ | |
| 302 | uniformDistribution.h fastaFormat.h gtrModel.h fromQtoPt.h | |
| 303 | KH_calculation.o KH_calculation.debug.o: KH_calculation.cpp KH_calculation.h definitions.h | |
| 304 | likeDist.o likeDist.debug.o: likeDist.cpp likeDist.h definitions.h countTableComponent.h \ | |
| 305 | distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 306 | someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 307 | replacementModel.h distribution.h jcDistance.h unObservableData.h tree.h \ | |
| 308 | readTree.h sequenceContainer.h gainLossAlphabet.h computePijComponent.h \ | |
| 309 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 310 | generalGammaDistribution.h numRec.h uniformDistribution.h | |
| 311 | likeDistfixRoot.o likeDistfixRoot.debug.o: likeDistfixRoot.cpp likeDistfixRoot.h definitions.h \ | |
| 312 | countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \ | |
| 313 | mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 314 | replacementModel.h distribution.h jcDistance.h sequenceContainer.h \ | |
| 315 | gainLossAlphabet.h unObservableData.h tree.h readTree.h \ | |
| 316 | computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \ | |
| 317 | generalGammaDistribution.h numRec.h uniformDistribution.h | |
| 318 | likeDistProp.o likeDistProp.debug.o: likeDistProp.cpp likeDistProp.h definitions.h \ | |
| 319 | countTableComponent.h stochasticProcess.h pijAccelerator.h \ | |
| 320 | replacementModel.h distribution.h numRec.h errorMsg.h \ | |
| 321 | uniformDistribution.h logFile.h | |
| 322 | likeDistPropEB.o likeDistPropEB.debug.o: likeDistPropEB.cpp likeDistPropEB.h definitions.h \ | |
| 323 | countTableComponent.h multipleStochasticProcess.h stochasticProcess.h \ | |
| 324 | pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \ | |
| 325 | generalGammaDistribution.h errorMsg.h logFile.h numRec.h \ | |
| 326 | uniformDistribution.h | |
| 327 | likelihoodComputation.o likelihoodComputation.debug.o: likelihoodComputation.cpp definitions.h tree.h \ | |
| 328 | readTree.h errorMsg.h logFile.h computeUpAlg.h suffStatComponent.h \ | |
| 329 | sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 330 | gainLossAlphabet.h computePijComponent.h stochasticProcess.h \ | |
| 331 | pijAccelerator.h replacementModel.h distribution.h \ | |
| 332 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 333 | generalGammaDistribution.h likelihoodComputation.h unObservableData.h \ | |
| 334 | gammaUtilities.h numRec.h uniformDistribution.h | |
| 335 | likelihoodComputationFactors.o likelihoodComputationFactors.debug.o: likelihoodComputationFactors.cpp \ | |
| 336 | definitions.h tree.h readTree.h errorMsg.h logFile.h computeUpAlg.h \ | |
| 337 | suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \ | |
| 338 | mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \ | |
| 339 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 340 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 341 | generalGammaDistribution.h likelihoodComputationFactors.h | |
| 342 | logFile.o logFile.debug.o: logFile.cpp logFile.h errorMsg.h | |
| 343 | maseFormat.o maseFormat.debug.o: maseFormat.cpp maseFormat.h sequenceContainer.h \ | |
| 344 | definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 345 | logFile.h gainLossAlphabet.h | |
| 346 | molphyFormat.o molphyFormat.debug.o: molphyFormat.cpp molphyFormat.h sequenceContainer.h \ | |
| 347 | definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 348 | logFile.h gainLossAlphabet.h | |
| 349 | nexusFormat.o nexusFormat.debug.o: nexusFormat.cpp nexusFormat.h sequenceContainer.h \ | |
| 350 | definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 351 | logFile.h gainLossAlphabet.h | |
| 352 | nj.o nj.debug.o: nj.cpp nj.h definitions.h tree.h readTree.h errorMsg.h logFile.h \ | |
| 353 | sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 354 | gainLossAlphabet.h njConstrain.h distances2Tree.h treeUtil.h | |
| 355 | njConstrain.o njConstrain.debug.o: njConstrain.cpp definitions.h njConstrain.h \ | |
| 356 | sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 357 | someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h | |
| 358 | nucJC.o nucJC.debug.o: nucJC.cpp nucJC.h replacementModel.h definitions.h | |
| 359 | nucleotide.o nucleotide.debug.o: nucleotide.cpp nucleotide.h definitions.h alphabet.h \ | |
| 360 | errorMsg.h | |
| 361 | numRec.o numRec.debug.o: numRec.cpp numRec.h definitions.h errorMsg.h \ | |
| 362 | uniformDistribution.h distribution.h logFile.h matrixUtils.h | |
| 363 | Parameters.o Parameters.debug.o: Parameters.cpp Parameters.h ConversionUtils.h definitions.h | |
| 364 | phylipFormat.o phylipFormat.debug.o: phylipFormat.cpp phylipFormat.h definitions.h \ | |
| 365 | sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 366 | someUtil.h logFile.h gainLossAlphabet.h | |
| 367 | pijAccelerator.o pijAccelerator.debug.o: pijAccelerator.cpp pijAccelerator.h definitions.h \ | |
| 368 | replacementModel.h | |
| 369 | readDatMatrix.o readDatMatrix.debug.o: readDatMatrix.cpp readDatMatrix.h definitions.h \ | |
| 370 | datMatrixHolder.h replacementModel.h errorMsg.h logFile.h fromQtoPt.h | |
| 371 | readTree.o readTree.debug.o: readTree.cpp definitions.h errorMsg.h someUtil.h logFile.h \ | |
| 372 | alphabet.h readTree.h | |
| 373 | recognizeFormat.o recognizeFormat.debug.o: recognizeFormat.cpp recognizeFormat.h \ | |
| 374 | sequenceContainer.h definitions.h sequence.h errorMsg.h alphabet.h \ | |
| 375 | mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h maseFormat.h \ | |
| 376 | molphyFormat.h phylipFormat.h nexusFormat.h fastaFormat.h \ | |
| 377 | clustalFormat.h phylipSequentialFormat.h | |
| 378 | replacementModel.o replacementModel.debug.o: replacementModel.cpp replacementModel.h definitions.h | |
| 379 | searchStatus.o searchStatus.debug.o: searchStatus.cpp searchStatus.h definitions.h | |
| 380 | seqContainerTreeMap.o seqContainerTreeMap.debug.o: seqContainerTreeMap.cpp seqContainerTreeMap.h \ | |
| 381 | definitions.h tree.h readTree.h errorMsg.h logFile.h treeIt.h \ | |
| 382 | sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 383 | gainLossAlphabet.h treeUtil.h | |
| 384 | sequence.o sequence.debug.o: sequence.cpp sequence.h definitions.h errorMsg.h alphabet.h \ | |
| 385 | mulAlphabet.h someUtil.h logFile.h | |
| 386 | sequenceContainer.o sequenceContainer.debug.o: sequenceContainer.cpp sequenceContainer.h \ | |
| 387 | definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 388 | logFile.h gainLossAlphabet.h fastaFormat.h | |
| 389 | simulateTree.o simulateTree.debug.o: simulateTree.cpp definitions.h treeUtil.h tree.h \ | |
| 390 | readTree.h errorMsg.h logFile.h simulateTree.h stochasticProcess.h \ | |
| 391 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 392 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 393 | talRandom.h gammaDistribution.h generalGammaDistribution.h codon.h \ | |
| 394 | geneticCodeHolder.h | |
| 395 | siteSpecificRate.o siteSpecificRate.debug.o: siteSpecificRate.cpp siteSpecificRate.h definitions.h \ | |
| 396 | tree.h readTree.h errorMsg.h logFile.h sequenceContainer.h sequence.h \ | |
| 397 | alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 398 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 399 | multipleStochasticProcess.h computePijComponent.h gammaDistribution.h \ | |
| 400 | generalGammaDistribution.h unObservableData.h numRec.h \ | |
| 401 | uniformDistribution.h checkcovFanctors.h likelihoodComputation.h \ | |
| 402 | suffStatComponent.h | |
| 403 | someUtil.o someUtil.debug.o: someUtil.cpp someUtil.h logFile.h definitions.h alphabet.h \ | |
| 404 | errorMsg.h talRandom.h | |
| 405 | split.o split.debug.o: split.cpp split.h definitions.h | |
| 406 | splitMap.o splitMap.debug.o: splitMap.cpp splitMap.h definitions.h split.h | |
| 407 | splitTreeUtil.o splitTreeUtil.debug.o: splitTreeUtil.cpp splitTreeUtil.h tree.h definitions.h \ | |
| 408 | readTree.h errorMsg.h logFile.h split.h someUtil.h alphabet.h | |
| 409 | stochasticProcess.o stochasticProcess.debug.o: stochasticProcess.cpp stochasticProcess.h \ | |
| 410 | pijAccelerator.h definitions.h replacementModel.h distribution.h \ | |
| 411 | errorMsg.h | |
| 412 | suffStatComponent.o suffStatComponent.debug.o: suffStatComponent.cpp suffStatComponent.h \ | |
| 413 | definitions.h | |
| 414 | talRandom.o talRandom.debug.o: talRandom.cpp talRandom.h definitions.h logFile.h | |
| 415 | tree.o tree.debug.o: tree.cpp definitions.h tree.h readTree.h errorMsg.h logFile.h \ | |
| 416 | treeUtil.h someUtil.h alphabet.h | |
| 417 | treeIt.o treeIt.debug.o: treeIt.cpp definitions.h treeIt.h errorMsg.h tree.h readTree.h \ | |
| 418 | logFile.h | |
| 419 | treeUtil.o treeUtil.debug.o: treeUtil.cpp definitions.h treeUtil.h tree.h readTree.h \ | |
| 420 | errorMsg.h logFile.h treeIt.h someUtil.h alphabet.h | |
| 421 | uniDistribution.o uniDistribution.debug.o: uniDistribution.cpp uniDistribution.h distribution.h \ | |
| 422 | definitions.h errorMsg.h | |
| 423 | uniformDistribution.o uniformDistribution.debug.o: uniformDistribution.cpp uniformDistribution.h \ | |
| 424 | definitions.h distribution.h | |
| 425 | cmdline2EvolObjs.o cmdline2EvolObjs.debug.o: cmdline2EvolObjs.cpp cmdline2EvolObjs.h amino.h \ | |
| 426 | definitions.h errorMsg.h alphabet.h geneticCodeHolder.h codon.h \ | |
| 427 | someUtil.h logFile.h nucleotide.h sequenceContainer.h sequence.h \ | |
| 428 | mulAlphabet.h gainLossAlphabet.h tree.h readTree.h stochasticProcess.h \ | |
| 429 | pijAccelerator.h replacementModel.h distribution.h uniDistribution.h \ | |
| 430 | trivialAccelerator.h alphaTrivialAccelerator.h readDatMatrix.h \ | |
| 431 | datMatrixHolder.h chebyshevAccelerator.h talRandom.h nucJC.h aaJC.h \ | |
| 432 | hky.h tamura92.h gtrModel.h fromQtoPt.h gammaDistribution.h \ | |
| 433 | generalGammaDistribution.h recognizeFormat.h replacementModelSSRV.h \ | |
| 434 | stochasticProcessSSRV.h | |
| 435 | generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.debug.o: generalGammaDistributionLaguerre.cpp \ | |
| 436 | generalGammaDistributionLaguerre.h definitions.h \ | |
| 437 | generalGammaDistribution.h distribution.h gammaUtilities.h numRec.h \ | |
| 438 | errorMsg.h uniformDistribution.h logFile.h GLaguer.h | |
| 439 | gammaDistributionLaguerre.o gammaDistributionLaguerre.debug.o: gammaDistributionLaguerre.cpp \ | |
| 440 | gammaDistributionLaguerre.h definitions.h \ | |
| 441 | generalGammaDistributionLaguerre.h generalGammaDistribution.h \ | |
| 442 | distribution.h errorMsg.h gammaUtilities.h numRec.h \ | |
| 443 | uniformDistribution.h logFile.h | |
| 444 | GLaguer.o GLaguer.debug.o: GLaguer.cpp definitions.h GLaguer.h errorMsg.h \ | |
| 445 | gammaUtilities.h numRec.h uniformDistribution.h distribution.h logFile.h | |
| 446 | givenRatesMLDistance.o givenRatesMLDistance.debug.o: givenRatesMLDistance.cpp givenRatesMLDistance.h \ | |
| 447 | definitions.h countTableComponent.h likeDist.h distanceMethod.h \ | |
| 448 | sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 449 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 450 | jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \ | |
| 451 | gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \ | |
| 452 | gammaDistribution.h generalGammaDistribution.h numRec.h \ | |
| 453 | uniformDistribution.h | |
| 454 | distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.debug.o: distanceBasedSeqs2Tree.cpp \ | |
| 455 | distanceBasedSeqs2Tree.h distanceMethod.h definitions.h sequence.h \ | |
| 456 | errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 457 | sequenceContainer.h gainLossAlphabet.h stochasticProcess.h \ | |
| 458 | pijAccelerator.h replacementModel.h distribution.h likeDist.h \ | |
| 459 | countTableComponent.h jcDistance.h unObservableData.h tree.h readTree.h \ | |
| 460 | computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \ | |
| 461 | generalGammaDistribution.h distances2Tree.h givenRatesMLDistance.h \ | |
| 462 | posteriorDistance.h uniDistribution.h distanceTable.h bestAlpha.h \ | |
| 463 | likelihoodComputation.h suffStatComponent.h siteSpecificRate.h bblEM.h \ | |
| 464 | tamura92.h bestTamura92param.h bestGtrModelParams.h gtrModel.h \ | |
| 465 | fromQtoPt.h replacementModelSSRV.h trivialAccelerator.h | |
| 466 | posteriorDistance.o posteriorDistance.debug.o: posteriorDistance.cpp posteriorDistance.h likeDist.h \ | |
| 467 | definitions.h countTableComponent.h distanceMethod.h sequence.h \ | |
| 468 | errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 469 | stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \ | |
| 470 | jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \ | |
| 471 | gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \ | |
| 472 | gammaDistribution.h generalGammaDistribution.h numRec.h \ | |
| 473 | uniformDistribution.h uniDistribution.h | |
| 474 | pairwiseGammaDistance.o pairwiseGammaDistance.debug.o: pairwiseGammaDistance.cpp \ | |
| 475 | pairwiseGammaDistance.h likeDist.h definitions.h countTableComponent.h \ | |
| 476 | distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 477 | someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 478 | replacementModel.h distribution.h jcDistance.h unObservableData.h tree.h \ | |
| 479 | readTree.h sequenceContainer.h gainLossAlphabet.h computePijComponent.h \ | |
| 480 | multipleStochasticProcess.h gammaDistribution.h \ | |
| 481 | generalGammaDistribution.h numRec.h uniformDistribution.h \ | |
| 482 | uniDistribution.h | |
| 483 | doubleRep.o doubleRep.debug.o: doubleRep.cpp | |
| 484 | logRep.o logRep.debug.o: logRep.cpp | |
| 485 | indel.o indel.debug.o: indel.cpp indel.h definitions.h errorMsg.h alphabet.h | |
| 486 | indelModel.o indelModel.debug.o: indelModel.cpp indelModel.h replacementModel.h \ | |
| 487 | definitions.h | |
| 488 | mulAlphabet.o mulAlphabet.debug.o: mulAlphabet.cpp mulAlphabet.h definitions.h alphabet.h \ | |
| 489 | someUtil.h logFile.h distribution.h errorMsg.h | |
| 490 | replacementModelSSRV.o replacementModelSSRV.debug.o: replacementModelSSRV.cpp replacementModelSSRV.h \ | |
| 491 | replacementModel.h definitions.h distribution.h fromQtoPt.h errorMsg.h \ | |
| 492 | logFile.h | |
| 493 | stochasticProcessSSRV.o stochasticProcessSSRV.debug.o: stochasticProcessSSRV.cpp \ | |
| 494 | stochasticProcessSSRV.h stochasticProcess.h pijAccelerator.h \ | |
| 495 | definitions.h replacementModel.h distribution.h replacementModelSSRV.h \ | |
| 496 | fromQtoPt.h errorMsg.h | |
| 497 | bestAlphaAndNu.o bestAlphaAndNu.debug.o: bestAlphaAndNu.cpp bestAlphaAndNu.h definitions.h \ | |
| 498 | sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 499 | someUtil.h logFile.h gainLossAlphabet.h stochasticProcess.h \ | |
| 500 | pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \ | |
| 501 | generalGammaDistribution.h tree.h readTree.h replacementModelSSRV.h \ | |
| 502 | fromQtoPt.h tamura92.h stochasticProcessSSRV.h C_evalParamUSSRV.h \ | |
| 503 | likelihoodComputation.h computePijComponent.h \ | |
| 504 | multipleStochasticProcess.h suffStatComponent.h unObservableData.h \ | |
| 505 | likelihoodComputation2USSRV.h ussrvModel.h computeUpAlg.h bestAlpha.h \ | |
| 506 | numRec.h uniformDistribution.h bblEM.h countTableComponent.h | |
| 507 | C_evalParamUSSRV.o C_evalParamUSSRV.debug.o: C_evalParamUSSRV.cpp C_evalParamUSSRV.h definitions.h \ | |
| 508 | likelihoodComputation.h computePijComponent.h tree.h readTree.h \ | |
| 509 | errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 510 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 511 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 512 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 513 | suffStatComponent.h unObservableData.h likelihoodComputation2USSRV.h \ | |
| 514 | ussrvModel.h stochasticProcessSSRV.h replacementModelSSRV.h fromQtoPt.h \ | |
| 515 | computeUpAlg.h tamura92.h | |
| 516 | matrixUtils.o matrixUtils.debug.o: matrixUtils.cpp matrixUtils.h definitions.h logFile.h \ | |
| 517 | errorMsg.h | |
| 518 | betaOmegaDistribution.o betaOmegaDistribution.debug.o: betaOmegaDistribution.cpp \ | |
| 519 | betaOmegaDistribution.h definitions.h distribution.h betaDistribution.h \ | |
| 520 | logFile.h gammaUtilities.h numRec.h errorMsg.h uniformDistribution.h \ | |
| 521 | betaUtilities.h | |
| 522 | betaUtilities.o betaUtilities.debug.o: betaUtilities.cpp definitions.h betaUtilities.h numRec.h \ | |
| 523 | errorMsg.h uniformDistribution.h distribution.h logFile.h \ | |
| 524 | gammaUtilities.h | |
| 525 | betaDistribution.o betaDistribution.debug.o: betaDistribution.cpp betaDistribution.h definitions.h \ | |
| 526 | distribution.h gammaUtilities.h numRec.h errorMsg.h \ | |
| 527 | uniformDistribution.h logFile.h betaUtilities.h | |
| 528 | geneticCodeHolder.o geneticCodeHolder.debug.o: geneticCodeHolder.cpp geneticCodeHolder.h \ | |
| 529 | replacementMatrixSource/nuclearStandard.code \ | |
| 530 | replacementMatrixSource/nuclearEuplotid.code \ | |
| 531 | replacementMatrixSource/nuclearCiliate.code \ | |
| 532 | replacementMatrixSource/nuclearBlepharisma.code \ | |
| 533 | replacementMatrixSource/mitochondriaYeast.code \ | |
| 534 | replacementMatrixSource/mitochondriaVertebrate.code \ | |
| 535 | replacementMatrixSource/mitochondriaProtozoan.code \ | |
| 536 | replacementMatrixSource/mitochondriaInvertebrate.code \ | |
| 537 | replacementMatrixSource/mitochondriaFlatworm.code \ | |
| 538 | replacementMatrixSource/mitochondriaEchinoderm.code \ | |
| 539 | replacementMatrixSource/mitochondriaAscidian.code | |
| 540 | samplingSequences.o samplingSequences.debug.o: samplingSequences.cpp samplingSequences.h \ | |
| 541 | definitions.h distanceMethod.h sequence.h errorMsg.h alphabet.h \ | |
| 542 | mulAlphabet.h someUtil.h logFile.h sequenceContainer.h \ | |
| 543 | gainLossAlphabet.h pDistance.h talRandom.h | |
| 544 | bblEM2USSRV.o bblEM2USSRV.debug.o: bblEM2USSRV.cpp bblEM2USSRV.h definitions.h tree.h \ | |
| 545 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 546 | replacementModel.h distribution.h sequenceContainer.h sequence.h \ | |
| 547 | alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 548 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 549 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 550 | ussrvModel.h stochasticProcessSSRV.h replacementModelSSRV.h fromQtoPt.h \ | |
| 551 | computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \ | |
| 552 | fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h \ | |
| 553 | distanceMethod.h likelihoodComputation2USSRV.h likelihoodComputation.h \ | |
| 554 | unObservableData.h | |
| 555 | bestParamUSSRV.o bestParamUSSRV.debug.o: bestParamUSSRV.cpp bestParamUSSRV.h definitions.h \ | |
| 556 | sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 557 | someUtil.h logFile.h gainLossAlphabet.h stochasticProcess.h \ | |
| 558 | pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \ | |
| 559 | generalGammaDistribution.h tree.h readTree.h replacementModelSSRV.h \ | |
| 560 | fromQtoPt.h stochasticProcessSSRV.h C_evalParamUSSRV.h \ | |
| 561 | likelihoodComputation.h computePijComponent.h \ | |
| 562 | multipleStochasticProcess.h suffStatComponent.h unObservableData.h \ | |
| 563 | likelihoodComputation2USSRV.h ussrvModel.h computeUpAlg.h tamura92.h \ | |
| 564 | bestAlpha.h numRec.h uniformDistribution.h bblEM.h countTableComponent.h \ | |
| 565 | bestAlphaAndNu.h bblEM2USSRV.h computeDownAlg.h computeCounts.h treeIt.h \ | |
| 566 | fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h \ | |
| 567 | distanceMethod.h | |
| 568 | likeDist2USSRV.o likeDist2USSRV.debug.o: likeDist2USSRV.cpp likeDist2USSRV.h definitions.h \ | |
| 569 | countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \ | |
| 570 | mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 571 | replacementModel.h distribution.h ussrvModel.h stochasticProcessSSRV.h \ | |
| 572 | replacementModelSSRV.h fromQtoPt.h gammaDistribution.h \ | |
| 573 | generalGammaDistribution.h numRec.h uniformDistribution.h | |
| 574 | ussrvModel.o ussrvModel.debug.o: ussrvModel.cpp ussrvModel.h stochasticProcessSSRV.h \ | |
| 575 | stochasticProcess.h pijAccelerator.h definitions.h replacementModel.h \ | |
| 576 | distribution.h replacementModelSSRV.h fromQtoPt.h errorMsg.h \ | |
| 577 | gammaDistribution.h generalGammaDistribution.h logFile.h | |
| 578 | likelihoodComputation2USSRV.o likelihoodComputation2USSRV.debug.o: likelihoodComputation2USSRV.cpp \ | |
| 579 | likelihoodComputation2USSRV.h definitions.h computePijComponent.h tree.h \ | |
| 580 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 581 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 582 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 583 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 584 | suffStatComponent.h ussrvModel.h stochasticProcessSSRV.h \ | |
| 585 | replacementModelSSRV.h fromQtoPt.h computeUpAlg.h \ | |
| 586 | likelihoodComputation.h unObservableData.h | |
| 587 | fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.debug.o: \ | |
| 588 | fromCountTableComponentToDistance2USSRV.cpp \ | |
| 589 | fromCountTableComponentToDistance2USSRV.h definitions.h \ | |
| 590 | countTableComponent.h stochasticProcess.h pijAccelerator.h \ | |
| 591 | replacementModel.h distribution.h ussrvModel.h stochasticProcessSSRV.h \ | |
| 592 | replacementModelSSRV.h fromQtoPt.h errorMsg.h gammaDistribution.h \ | |
| 593 | generalGammaDistribution.h logFile.h likeDist2USSRV.h distanceMethod.h \ | |
| 594 | sequence.h alphabet.h mulAlphabet.h someUtil.h likeDist.h jcDistance.h \ | |
| 595 | unObservableData.h tree.h readTree.h sequenceContainer.h \ | |
| 596 | gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h | |
| 597 | normalDist.o normalDist.debug.o: normalDist.cpp normalDist.h definitions.h | |
| 598 | tamura92.o tamura92.debug.o: tamura92.cpp tamura92.h replacementModel.h definitions.h \ | |
| 599 | errorMsg.h | |
| 600 | bestTamura92param.o bestTamura92param.debug.o: bestTamura92param.cpp bestTamura92param.h \ | |
| 601 | definitions.h likelihoodComputation.h computePijComponent.h tree.h \ | |
| 602 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 603 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 604 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 605 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 606 | suffStatComponent.h unObservableData.h tamura92.h bblEM.h \ | |
| 607 | countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \ | |
| 608 | numRec.h uniformDistribution.h bestAlpha.h | |
| 609 | phylipSequentialFormat.o phylipSequentialFormat.debug.o: phylipSequentialFormat.cpp \ | |
| 610 | phylipSequentialFormat.h definitions.h sequenceContainer.h sequence.h \ | |
| 611 | errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 612 | gainLossAlphabet.h | |
| 613 | simulateCodonsJumps.o simulateCodonsJumps.debug.o: simulateCodonsJumps.cpp simulateCodonsJumps.h \ | |
| 614 | simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \ | |
| 615 | logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 616 | distribution.h alphabet.h codon.h someUtil.h geneticCodeHolder.h \ | |
| 617 | talRandom.h | |
| 618 | simulateJumpsAbstract.o simulateJumpsAbstract.debug.o: simulateJumpsAbstract.cpp \ | |
| 619 | simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \ | |
| 620 | logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 621 | distribution.h alphabet.h | |
| 622 | ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.debug.o: ssrvDistanceSeqs2Tree.cpp \ | |
| 623 | ssrvDistanceSeqs2Tree.h distanceBasedSeqs2Tree.h distanceMethod.h \ | |
| 624 | definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 625 | logFile.h sequenceContainer.h gainLossAlphabet.h stochasticProcess.h \ | |
| 626 | pijAccelerator.h replacementModel.h distribution.h likeDist.h \ | |
| 627 | countTableComponent.h jcDistance.h unObservableData.h tree.h readTree.h \ | |
| 628 | computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \ | |
| 629 | generalGammaDistribution.h distances2Tree.h givenRatesMLDistance.h \ | |
| 630 | posteriorDistance.h bestParamUSSRV.h replacementModelSSRV.h fromQtoPt.h \ | |
| 631 | stochasticProcessSSRV.h C_evalParamUSSRV.h likelihoodComputation.h \ | |
| 632 | suffStatComponent.h likelihoodComputation2USSRV.h ussrvModel.h \ | |
| 633 | computeUpAlg.h tamura92.h bestAlpha.h numRec.h uniformDistribution.h \ | |
| 634 | bblEM.h bestAlphaAndNu.h bblEM2USSRV.h computeDownAlg.h computeCounts.h \ | |
| 635 | treeIt.h fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h | |
| 636 | multipleStochasticProcess.o multipleStochasticProcess.debug.o: multipleStochasticProcess.cpp \ | |
| 637 | multipleStochasticProcess.h stochasticProcess.h pijAccelerator.h \ | |
| 638 | definitions.h replacementModel.h distribution.h errorMsg.h | |
| 639 | distributionPlusInvariant.o distributionPlusInvariant.debug.o: distributionPlusInvariant.cpp definitions.h \ | |
| 640 | distributionPlusInvariant.h distribution.h errorMsg.h logFile.h | |
| 641 | extremeValDistribution.o extremeValDistribution.debug.o: extremeValDistribution.cpp \ | |
| 642 | extremeValDistribution.h definitions.h | |
| 643 | gammaDistributionFixedCategories.o gammaDistributionFixedCategories.debug.o: gammaDistributionFixedCategories.cpp \ | |
| 644 | gammaDistributionFixedCategories.h definitions.h \ | |
| 645 | generalGammaDistributionFixedCategories.h generalGammaDistribution.h \ | |
| 646 | distribution.h errorMsg.h gammaUtilities.h numRec.h \ | |
| 647 | uniformDistribution.h logFile.h matrixUtils.h | |
| 648 | generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.debug.o: \ | |
| 649 | generalGammaDistributionPlusInvariant.cpp \ | |
| 650 | generalGammaDistributionPlusInvariant.h definitions.h \ | |
| 651 | distributionPlusInvariant.h distribution.h generalGammaDistribution.h \ | |
| 652 | errorMsg.h gammaUtilities.h numRec.h uniformDistribution.h logFile.h | |
| 653 | gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.debug.o: gammaDistributionPlusInvariant.cpp \ | |
| 654 | gammaDistributionPlusInvariant.h definitions.h \ | |
| 655 | distributionPlusInvariant.h distribution.h gammaDistribution.h \ | |
| 656 | generalGammaDistribution.h errorMsg.h gammaUtilities.h numRec.h \ | |
| 657 | uniformDistribution.h logFile.h | |
| 658 | distributionPlusCategory.o distributionPlusCategory.debug.o: distributionPlusCategory.cpp \ | |
| 659 | distributionPlusCategory.h definitions.h distribution.h logFile.h \ | |
| 660 | errorMsg.h | |
| 661 | simulateJumps.o simulateJumps.debug.o: simulateJumps.cpp simulateJumps.h \ | |
| 662 | simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \ | |
| 663 | logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 664 | distribution.h alphabet.h talRandom.h someUtil.h | |
| 665 | computeJumps.o computeJumps.debug.o: computeJumps.cpp computeJumps.h definitions.h tree.h \ | |
| 666 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 667 | replacementModel.h distribution.h alphabet.h someUtil.h talRandom.h \ | |
| 668 | matrixUtils.h | |
| 669 | seqeuncesFilter.o seqeuncesFilter.debug.o: seqeuncesFilter.cpp seqeuncesFilter.h definitions.h \ | |
| 670 | sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \ | |
| 671 | someUtil.h logFile.h gainLossAlphabet.h codon.h geneticCodeHolder.h \ | |
| 672 | amino.h fastaFormat.h nucleotide.h | |
| 673 | optGammaMixtureLS.o optGammaMixtureLS.debug.o: optGammaMixtureLS.cpp optGammaMixtureLS.h \ | |
| 674 | definitions.h suffStatGammaMixture.h stochasticProcess.h \ | |
| 675 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 676 | sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 677 | gainLossAlphabet.h tree.h readTree.h mixtureDistribution.h \ | |
| 678 | generalGammaDistribution.h computePijComponent.h \ | |
| 679 | multipleStochasticProcess.h gammaDistribution.h gammaUtilities.h \ | |
| 680 | numRec.h uniformDistribution.h likelihoodComputation.h \ | |
| 681 | suffStatComponent.h unObservableData.h | |
| 682 | mixtureDistribution.o mixtureDistribution.debug.o: mixtureDistribution.cpp mixtureDistribution.h \ | |
| 683 | definitions.h generalGammaDistribution.h distribution.h \ | |
| 684 | generalGammaDistributionLaguerre.h talRandom.h logFile.h someUtil.h \ | |
| 685 | alphabet.h errorMsg.h | |
| 686 | suffStatGammaMixture.o suffStatGammaMixture.debug.o: suffStatGammaMixture.cpp suffStatGammaMixture.h \ | |
| 687 | definitions.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 688 | distribution.h sequenceContainer.h sequence.h errorMsg.h alphabet.h \ | |
| 689 | mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \ | |
| 690 | mixtureDistribution.h generalGammaDistribution.h computePijComponent.h \ | |
| 691 | multipleStochasticProcess.h gammaDistribution.h likelihoodComputation.h \ | |
| 692 | suffStatComponent.h unObservableData.h gammaUtilities.h numRec.h \ | |
| 693 | uniformDistribution.h uniDistribution.h | |
| 694 | GamMixtureOptimizer.o GamMixtureOptimizer.debug.o: GamMixtureOptimizer.cpp GamMixtureOptimizer.h \ | |
| 695 | definitions.h stochasticProcess.h pijAccelerator.h replacementModel.h \ | |
| 696 | distribution.h sequenceContainer.h sequence.h errorMsg.h alphabet.h \ | |
| 697 | mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \ | |
| 698 | mixtureDistribution.h generalGammaDistribution.h unObservableData.h \ | |
| 699 | computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \ | |
| 700 | optGammaMixtureEM.h suffStatGammaMixture.h gammaUtilities.h numRec.h \ | |
| 701 | uniformDistribution.h optGammaMixtureLS.h likelihoodComputation.h \ | |
| 702 | suffStatComponent.h | |
| 703 | optGammaMixtureEM.o optGammaMixtureEM.debug.o: optGammaMixtureEM.cpp optGammaMixtureEM.h \ | |
| 704 | definitions.h suffStatGammaMixture.h stochasticProcess.h \ | |
| 705 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 706 | sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 707 | gainLossAlphabet.h tree.h readTree.h mixtureDistribution.h \ | |
| 708 | generalGammaDistribution.h computePijComponent.h \ | |
| 709 | multipleStochasticProcess.h gammaDistribution.h gammaUtilities.h \ | |
| 710 | numRec.h uniformDistribution.h likelihoodComputation.h \ | |
| 711 | suffStatComponent.h unObservableData.h uniDistribution.h | |
| 712 | gainLossAlphabet.o gainLossAlphabet.debug.o: gainLossAlphabet.cpp gainLossAlphabet.h alphabet.h \ | |
| 713 | errorMsg.h | |
| 714 | wYangModel.o wYangModel.debug.o: wYangModel.cpp wYangModel.h replacementModel.h \ | |
| 715 | definitions.h fromQtoPt.h codon.h errorMsg.h someUtil.h logFile.h \ | |
| 716 | alphabet.h geneticCodeHolder.h readDatMatrix.h datMatrixHolder.h | |
| 717 | codonUtils.o codonUtils.debug.o: codonUtils.cpp codonUtils.h nucleotide.h definitions.h \ | |
| 718 | alphabet.h codon.h errorMsg.h someUtil.h logFile.h geneticCodeHolder.h \ | |
| 719 | amino.h fastaFormat.h sequenceContainer.h sequence.h mulAlphabet.h \ | |
| 720 | gainLossAlphabet.h clustalFormat.h recognizeFormat.h stochasticProcess.h \ | |
| 721 | pijAccelerator.h replacementModel.h distribution.h wYangModel.h \ | |
| 722 | fromQtoPt.h evaluateCharacterFreq.h numRec.h uniformDistribution.h | |
| 723 | likelihoodComputation2Codon.o likelihoodComputation2Codon.debug.o: likelihoodComputation2Codon.cpp \ | |
| 724 | likelihoodComputation2Codon.h definitions.h computePijComponent.h tree.h \ | |
| 725 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 726 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 727 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 728 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 729 | suffStatComponent.h wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h \ | |
| 730 | computeUpAlg.h likelihoodComputation.h unObservableData.h | |
| 731 | likeDist2Codon.o likeDist2Codon.debug.o: likeDist2Codon.cpp likeDist2Codon.h definitions.h \ | |
| 732 | countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \ | |
| 733 | mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 734 | replacementModel.h distribution.h wYangModel.h fromQtoPt.h codon.h \ | |
| 735 | geneticCodeHolder.h numRec.h uniformDistribution.h | |
| 736 | unObservableData.o unObservableData.debug.o: unObservableData.cpp unObservableData.h definitions.h \ | |
| 737 | tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \ | |
| 738 | pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \ | |
| 739 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 740 | computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \ | |
| 741 | generalGammaDistribution.h likelihoodComputation.h suffStatComponent.h \ | |
| 742 | likelihoodComputationGL.h computeUpAlg.h | |
| 743 | likelihoodComputationGL.o likelihoodComputationGL.debug.o: likelihoodComputationGL.cpp \ | |
| 744 | likelihoodComputationGL.h definitions.h computePijComponent.h tree.h \ | |
| 745 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 746 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 747 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 748 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 749 | suffStatComponent.h unObservableData.h computeUpAlg.h \ | |
| 750 | likelihoodComputation.h | |
| 751 | threeStateModel.o threeStateModel.debug.o: threeStateModel.cpp threeStateModel.h definitions.h \ | |
| 752 | replacementModel.h fromQtoPt.h errorMsg.h matrixUtils.h logFile.h \ | |
| 753 | someUtil.h alphabet.h | |
| 754 | threeStateAlphabet.o threeStateAlphabet.debug.o: threeStateAlphabet.cpp threeStateAlphabet.h \ | |
| 755 | alphabet.h errorMsg.h | |
| 756 | oneTwoMoreModel.o oneTwoMoreModel.debug.o: oneTwoMoreModel.cpp oneTwoMoreModel.h definitions.h \ | |
| 757 | replacementModel.h fromQtoPt.h errorMsg.h matrixUtils.h logFile.h \ | |
| 758 | someUtil.h alphabet.h | |
| 759 | betaDistributionFixedCategories.o betaDistributionFixedCategories.debug.o: betaDistributionFixedCategories.cpp \ | |
| 760 | betaDistributionFixedCategories.h definitions.h betaDistribution.h \ | |
| 761 | distribution.h errorMsg.h gammaUtilities.h numRec.h \ | |
| 762 | uniformDistribution.h logFile.h | |
| 763 | betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.debug.o: \ | |
| 764 | betaDistributionFixedCategoriesWithOmegaUniform.cpp \ | |
| 765 | betaDistributionFixedCategoriesWithOmegaUniform.h definitions.h \ | |
| 766 | betaDistributionFixedCategories.h betaDistribution.h distribution.h \ | |
| 767 | errorMsg.h uniformDistribution.h gammaUtilities.h numRec.h logFile.h \ | |
| 768 | matrixUtils.h | |
| 769 | bblEM2codon.o bblEM2codon.debug.o: bblEM2codon.cpp bblEM2codon.h definitions.h tree.h \ | |
| 770 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 771 | replacementModel.h distribution.h sequenceContainer.h sequence.h \ | |
| 772 | alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 773 | countTableComponent.h computePijComponent.h multipleStochasticProcess.h \ | |
| 774 | gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \ | |
| 775 | likelihoodComputation.h unObservableData.h likelihoodComputation2Codon.h \ | |
| 776 | fromCountTableComponentToDistance2Codon.h computeUpAlg.h \ | |
| 777 | computeDownAlg.h computeCounts.h treeIt.h | |
| 778 | bestAlphaAndK.o bestAlphaAndK.debug.o: bestAlphaAndK.cpp bestAlphaAndK.h definitions.h tree.h \ | |
| 779 | readTree.h errorMsg.h logFile.h likelihoodComputation.h \ | |
| 780 | computePijComponent.h stochasticProcess.h pijAccelerator.h \ | |
| 781 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 782 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 783 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 784 | suffStatComponent.h unObservableData.h likelihoodComputation2Codon.h \ | |
| 785 | wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h bblEM2codon.h \ | |
| 786 | countTableComponent.h computeUpAlg.h numRec.h uniformDistribution.h \ | |
| 787 | betaOmegaDistribution.h betaDistribution.h codonUtils.h nucleotide.h \ | |
| 788 | amino.h fastaFormat.h clustalFormat.h recognizeFormat.h \ | |
| 789 | evaluateCharacterFreq.h | |
| 790 | fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.debug.o: \ | |
| 791 | fromCountTableComponentToDistance2Codon.cpp \ | |
| 792 | fromCountTableComponentToDistance2Codon.h definitions.h \ | |
| 793 | countTableComponent.h stochasticProcess.h pijAccelerator.h \ | |
| 794 | replacementModel.h distribution.h likeDist2Codon.h distanceMethod.h \ | |
| 795 | sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \ | |
| 796 | wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h likeDist.h \ | |
| 797 | jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \ | |
| 798 | gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \ | |
| 799 | gammaDistribution.h generalGammaDistribution.h | |
| 800 | gtrModel.o gtrModel.debug.o: gtrModel.cpp gtrModel.h replacementModel.h definitions.h \ | |
| 801 | fromQtoPt.h readDatMatrix.h datMatrixHolder.h errorMsg.h matrixUtils.h \ | |
| 802 | logFile.h | |
| 803 | bestGtrModelParams.o bestGtrModelParams.debug.o: bestGtrModelParams.cpp bestGtrModelParams.h \ | |
| 804 | definitions.h likelihoodComputation.h computePijComponent.h tree.h \ | |
| 805 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 806 | replacementModel.h distribution.h multipleStochasticProcess.h \ | |
| 807 | gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \ | |
| 808 | sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \ | |
| 809 | suffStatComponent.h unObservableData.h gtrModel.h fromQtoPt.h bblEM.h \ | |
| 810 | countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \ | |
| 811 | numRec.h uniformDistribution.h bestAlpha.h | |
| 812 | simulateRateShiftJumps.o simulateRateShiftJumps.debug.o: simulateRateShiftJumps.cpp \ | |
| 813 | simulateRateShiftJumps.h simulateJumpsAbstract.h definitions.h tree.h \ | |
| 814 | readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \ | |
| 815 | replacementModel.h distribution.h alphabet.h mulAlphabet.h someUtil.h \ | |
| 816 | talRandom.h replacementModelSSRV.h fromQtoPt.h \ | |
| 817 | generalGammaDistribution.h | |
| 818 | integerAlphabet.o integerAlphabet.debug.o: integerAlphabet.cpp integerAlphabet.h alphabet.h \ | |
| 819 | errorMsg.h logFile.h someUtil.h definitions.h |
| 0 | // $Id: someUtil.cpp 11906 2013-12-26 10:12:24Z itaymay $ | |
| 0 | // $Id: someUtil.cpp 15479 2016-10-10 16:25:21Z elilevy $ | |
| 1 | 1 | |
| 2 | 2 | #include "someUtil.h" |
| 3 | 3 | #include "errorMsg.h" |
| 225 | 225 | string double2string(const double x, const int lenght, bool round){ |
| 226 | 226 | |
| 227 | 227 | // first getting the integer part: |
| 228 | //Itay: fixing bug regarding negative floats | |
| 229 | 228 | double x_abs = fabs(x); |
| 230 | 229 | int theIntegerPart = static_cast<int>(x_abs); |
| 231 | 230 | double theRemainingPart = fabs(x_abs-theIntegerPart); |
| 232 | 231 | int integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght)); |
| 233 | if (round) | |
| 232 | if (round) { | |
| 234 | 233 | integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght)+0.5); |
| 234 | if (integerRepresentingTheRemainingPart == pow(10.0,lenght)) { | |
| 235 | integerRepresentingTheRemainingPart = 0; | |
| 236 | theIntegerPart++; | |
| 237 | } | |
| 238 | } | |
| 235 | 239 | |
| 236 | 240 | string part1 = int2string(theIntegerPart); |
| 237 | 241 | string part2 = int2string(integerRepresentingTheRemainingPart); |
| 352 | 356 | |
| 353 | 357 | bool checkThatFileExist(const string& fileName) { |
| 354 | 358 | ifstream file1(fileName.c_str()); |
| 355 | if (file1==NULL) return false; | |
| 359 | if (!file1.good()) return false; | |
| 356 | 360 | file1.close(); |
| 357 | 361 | return true; |
| 358 | 362 | } |
| 400 | 404 | const string& inFileName) { |
| 401 | 405 | ifstream f; |
| 402 | 406 | f.open(inFileName.c_str()); |
| 403 | if (f==NULL) { | |
| 407 | if (!f.good()) { | |
| 404 | 408 | string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; |
| 405 | 409 | errorMsg::reportError(tmp); |
| 406 | 410 | } |
| 427 | 431 | const string& inFileName) {// return the string that is AFTER the string to search. |
| 428 | 432 | ifstream f; |
| 429 | 433 | f.open(inFileName.c_str()); |
| 430 | if (f==NULL) { | |
| 434 | if (!f.good()) { | |
| 431 | 435 | string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; |
| 432 | 436 | errorMsg::reportError(tmp); |
| 433 | 437 | } |
| 451 | 455 | bool doesWordExistInFile(const string& string2find,const string& inFileName) { |
| 452 | 456 | ifstream f; |
| 453 | 457 | f.open(inFileName.c_str()); |
| 454 | if (f==NULL) { | |
| 458 | if (!f.good()) { | |
| 455 | 459 | string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; |
| 456 | 460 | errorMsg::reportError(tmp); |
| 457 | 461 | } |
| 52 | 52 | |
| 53 | 53 | .SECONDARY: $(addsuffix _cmdline.c,$(EXEC)) $(addsuffix _cmdline.h,$(EXEC)) $(addsuffix .ggo,$(EXEC)) |
| 54 | 54 | |
| 55 | CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32 | |
| 56 | CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32 | |
| 55 | CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG | |
| 56 | CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG | |
| 57 | 57 | |
| 58 | 58 | LDFLAGSDEBUG := $(LDFLAGS) -g |
| 59 | 59 | # sources |
| 195 | 195 | echo $(LIB) |
| 196 | 196 | |
| 197 | 197 | |
| 198 | %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG -ftemplate-depth-25 | |
| 198 | %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG | |
| 199 | 199 | |
| 200 | 200 | %.debug: %.o |
| 201 | 201 | |
| 46 | 46 | //} |
| 47 | 47 | out<<" position is: "<<_position<<endl; |
| 48 | 48 | // cerr<<"reportFileIs: "<<_reportFileName<<endl; |
| 49 | if (out == NULL) { | |
| 49 | if (!out.good()) { | |
| 50 | 50 | errorMsg::reportError("unable to open output file for reporting"); |
| 51 | 51 | } |
| 52 | 52 | // exit(555); |
| 0 | fastml.o fastml.debug.o: fastml.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \ | |
| 1 | ../../libs/phylogeny/definitions.h bb_options_list.h \ | |
| 2 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 3 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \ | |
| 4 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \ | |
| 5 | ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \ | |
| 6 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 7 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 8 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 9 | ../../libs/phylogeny/replacementModel.h \ | |
| 10 | ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \ | |
| 11 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \ | |
| 12 | ../../libs/phylogeny/geneticCodeHolder.h \ | |
| 13 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/logFile.h \ | |
| 14 | sequenceDataDiff.h ../../libs/phylogeny/amino.h \ | |
| 15 | ../../libs/phylogeny/codon.h ../../libs/phylogeny/recognizeFormat.h \ | |
| 16 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 17 | ../../libs/phylogeny/uniDistribution.h \ | |
| 18 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 19 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 20 | ../../libs/phylogeny/replacementModel.h \ | |
| 21 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 22 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 23 | ../../libs/phylogeny/chebyshevAccelerator.h bbAlg.h \ | |
| 24 | ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \ | |
| 25 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 26 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 27 | ../../libs/phylogeny/gammaDistribution.h bbNodeOrderAlg.h \ | |
| 28 | ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \ | |
| 29 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 30 | bbfindBestAVDynProg.h bbReport.h ../../libs/phylogeny/distribution.h | |
| 31 | bbAlg.o bbAlg.debug.o: bbAlg.cpp bbAlg.h ../../libs/phylogeny/computePijComponent.h \ | |
| 32 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 33 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 34 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 35 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 36 | ../../libs/phylogeny/replacementModel.h \ | |
| 37 | ../../libs/phylogeny/distribution.h \ | |
| 38 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 39 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 40 | ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \ | |
| 41 | ../../libs/phylogeny/definitions.h bb_options.h \ | |
| 42 | ../../libs/phylogeny/getopt.h bb_options_list.h \ | |
| 43 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \ | |
| 44 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 45 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 46 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 47 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 48 | ../../libs/phylogeny/gainLossAlphabet.h bbEvaluateSpecificAV.h \ | |
| 49 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 50 | ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \ | |
| 51 | bbReport.h ../../libs/phylogeny/distribution.h \ | |
| 52 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 53 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 54 | ../../libs/phylogeny/computePijComponent.h \ | |
| 55 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 56 | ../../libs/phylogeny/unObservableData.h \ | |
| 57 | ../../libs/phylogeny/maseFormat.h | |
| 58 | bbComputeDownAlg.o bbComputeDownAlg.debug.o: bbComputeDownAlg.cpp bbComputeDownAlg.h \ | |
| 59 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \ | |
| 60 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 61 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/sequenceContainer.h \ | |
| 62 | ../../libs/phylogeny/sequence.h ../../libs/phylogeny/alphabet.h \ | |
| 63 | ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \ | |
| 64 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 65 | ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \ | |
| 66 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 67 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 68 | ../../libs/phylogeny/replacementModel.h \ | |
| 69 | ../../libs/phylogeny/distribution.h \ | |
| 70 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 71 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 72 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 73 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \ | |
| 74 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 75 | ../../libs/phylogeny/sequenceContainer.h | |
| 76 | bbComputeUpAlg.o bbComputeUpAlg.debug.o: bbComputeUpAlg.cpp bbComputeUpAlg.h \ | |
| 77 | ../../libs/phylogeny/computePijComponent.h \ | |
| 78 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 79 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 80 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 81 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 82 | ../../libs/phylogeny/replacementModel.h \ | |
| 83 | ../../libs/phylogeny/distribution.h \ | |
| 84 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 85 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 86 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 87 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/tree.h \ | |
| 88 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 89 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 90 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 91 | ../../libs/phylogeny/sequence.h \ | |
| 92 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 93 | ../../libs/phylogeny/sequenceContainer.h | |
| 94 | bbEvaluateSpecificAV.o bbEvaluateSpecificAV.debug.o: bbEvaluateSpecificAV.cpp bbEvaluateSpecificAV.h \ | |
| 95 | bb_options.h ../../libs/phylogeny/getopt.h \ | |
| 96 | ../../libs/phylogeny/definitions.h bb_options_list.h \ | |
| 97 | ../../libs/phylogeny/computePijComponent.h \ | |
| 98 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 99 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 100 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 101 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 102 | ../../libs/phylogeny/replacementModel.h \ | |
| 103 | ../../libs/phylogeny/distribution.h \ | |
| 104 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 105 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 106 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 107 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \ | |
| 108 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 109 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/sequenceContainer.h \ | |
| 110 | ../../libs/phylogeny/sequence.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 111 | ../../libs/phylogeny/stochasticProcess.h ../../libs/phylogeny/tree.h \ | |
| 112 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 113 | ../../libs/phylogeny/sequenceContainer.h | |
| 114 | bbfindBestAVDynProg.o bbfindBestAVDynProg.debug.o: bbfindBestAVDynProg.cpp bbfindBestAVDynProg.h \ | |
| 115 | bb_options.h ../../libs/phylogeny/getopt.h \ | |
| 116 | ../../libs/phylogeny/definitions.h bb_options_list.h \ | |
| 117 | ../../libs/phylogeny/computePijComponent.h \ | |
| 118 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 119 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 120 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 121 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 122 | ../../libs/phylogeny/replacementModel.h \ | |
| 123 | ../../libs/phylogeny/distribution.h \ | |
| 124 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 125 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 126 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 127 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \ | |
| 128 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 129 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 130 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 131 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 132 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 133 | ../../libs/phylogeny/sequenceContainer.h | |
| 134 | bbNodeOrderAlg.o bbNodeOrderAlg.debug.o: bbNodeOrderAlg.cpp bbNodeOrderAlg.h \ | |
| 135 | ../../libs/phylogeny/definitions.h bb_options.h \ | |
| 136 | ../../libs/phylogeny/getopt.h bb_options_list.h \ | |
| 137 | ../../libs/phylogeny/computePijComponent.h \ | |
| 138 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 139 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 140 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 141 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 142 | ../../libs/phylogeny/replacementModel.h \ | |
| 143 | ../../libs/phylogeny/distribution.h \ | |
| 144 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 145 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 146 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 147 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \ | |
| 148 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 149 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 150 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 151 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 152 | ../../libs/phylogeny/gainLossAlphabet.h bbComputeUpAlg.h \ | |
| 153 | bbComputeDownAlg.h ../../libs/phylogeny/computeMarginalAlg.h \ | |
| 154 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 155 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 156 | ../../libs/phylogeny/computePijComponent.h | |
| 157 | bb_options.o bb_options.debug.o: bb_options.cpp bb_options.h ../../libs/phylogeny/getopt.h \ | |
| 158 | ../../libs/phylogeny/definitions.h bb_options_list.h \ | |
| 159 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h | |
| 160 | bbReport.o bbReport.debug.o: bbReport.cpp bbReport.h ../../libs/phylogeny/definitions.h \ | |
| 161 | ../../libs/phylogeny/amino.h ../../libs/phylogeny/definitions.h \ | |
| 162 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \ | |
| 163 | ../../libs/phylogeny/geneticCodeHolder.h ../../libs/phylogeny/codon.h \ | |
| 164 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \ | |
| 165 | ../../libs/phylogeny/nucleotide.h ../../libs/phylogeny/codon.h | |
| 166 | computeMarginalReconstruction.o computeMarginalReconstruction.debug.o: computeMarginalReconstruction.cpp \ | |
| 167 | computeMarginalReconstruction.h ../../libs/phylogeny/definitions.h \ | |
| 168 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \ | |
| 169 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 170 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 171 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 172 | ../../libs/phylogeny/replacementModel.h \ | |
| 173 | ../../libs/phylogeny/distribution.h \ | |
| 174 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 175 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 176 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 177 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 178 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/tree.h \ | |
| 179 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 180 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 181 | ../../libs/phylogeny/computePijComponent.h \ | |
| 182 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 183 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 184 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 185 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 186 | ../../libs/phylogeny/computePijComponent.h \ | |
| 187 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 188 | ../../libs/phylogeny/computeMarginalAlg.h ../../libs/phylogeny/treeIt.h | |
| 189 | jointNoGamma.o jointNoGamma.debug.o: jointNoGamma.cpp jointNoGamma.h \ | |
| 190 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 191 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/readTree.h \ | |
| 192 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \ | |
| 193 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 194 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 195 | ../../libs/phylogeny/replacementModel.h \ | |
| 196 | ../../libs/phylogeny/distribution.h \ | |
| 197 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 198 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 199 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 200 | ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \ | |
| 201 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 202 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 203 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 204 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 205 | ../../libs/phylogeny/suffStatComponent.h suffStatComponentJointNoGamma.h \ | |
| 206 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/seqContainerTreeMap.h \ | |
| 207 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/sequenceContainer.h | |
| 208 | mainbb.o mainbb.debug.o: mainbb.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \ | |
| 209 | ../../libs/phylogeny/definitions.h bb_options_list.h \ | |
| 210 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 211 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \ | |
| 212 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \ | |
| 213 | ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \ | |
| 214 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 215 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 216 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 217 | ../../libs/phylogeny/replacementModel.h \ | |
| 218 | ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \ | |
| 219 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \ | |
| 220 | ../../libs/phylogeny/geneticCodeHolder.h \ | |
| 221 | ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/aaJC.h \ | |
| 222 | ../../libs/phylogeny/amino.h ../../libs/phylogeny/codon.h bbAlg.h \ | |
| 223 | ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \ | |
| 224 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 225 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 226 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 227 | ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \ | |
| 228 | ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \ | |
| 229 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 230 | ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \ | |
| 231 | bbReport.h ../../libs/phylogeny/distribution.h \ | |
| 232 | ../../libs/phylogeny/bestAlpha.h \ | |
| 233 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 234 | ../../libs/phylogeny/computePijComponent.h \ | |
| 235 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 236 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bblEM.h \ | |
| 237 | ../../libs/phylogeny/countTableComponent.h \ | |
| 238 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 239 | ../../libs/phylogeny/clustalFormat.h computeMarginalReconstruction.h \ | |
| 240 | ../../libs/phylogeny/distanceTable.h \ | |
| 241 | ../../libs/phylogeny/distanceMethod.h ../../libs/phylogeny/fastaFormat.h \ | |
| 242 | ../../libs/phylogeny/gammaDistribution.h jointNoGamma.h \ | |
| 243 | suffStatComponentJointNoGamma.h ../../libs/phylogeny/likeDist.h \ | |
| 244 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/logFile.h \ | |
| 245 | ../../libs/phylogeny/maseFormat.h ../../libs/phylogeny/molphyFormat.h \ | |
| 246 | ../../libs/phylogeny/nexusFormat.h ../../libs/phylogeny/nucleotide.h \ | |
| 247 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/nj.h \ | |
| 248 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 249 | ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/gtrModel.h \ | |
| 250 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/hky.h \ | |
| 251 | ../../libs/phylogeny/phylipFormat.h ../../libs/phylogeny/readDatMatrix.h \ | |
| 252 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 253 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 254 | ../../libs/phylogeny/trivialAccelerator.h \ | |
| 255 | ../../libs/phylogeny/uniDistribution.h \ | |
| 256 | ../../libs/phylogeny/bestGtrModelParams.h \ | |
| 257 | ../../libs/phylogeny/gtrModel.h ../../libs/phylogeny/bestTamura92param.h \ | |
| 258 | ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/bestHKYparam.h \ | |
| 259 | ../../libs/phylogeny/hky.h ../../libs/phylogeny/bestAlphaAndK.h \ | |
| 260 | ../../libs/phylogeny/likelihoodComputation2Codon.h \ | |
| 261 | ../../libs/phylogeny/wYangModel.h ../../libs/phylogeny/bblEM2codon.h \ | |
| 262 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \ | |
| 263 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 264 | ../../libs/phylogeny/codonUtils.h ../../libs/phylogeny/nucleotide.h \ | |
| 265 | ../../libs/phylogeny/amino.h ../../libs/phylogeny/fastaFormat.h \ | |
| 266 | ../../libs/phylogeny/clustalFormat.h \ | |
| 267 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 268 | ../../libs/phylogeny/evaluateCharacterFreq.h | |
| 269 | sequenceDataDiff.o sequenceDataDiff.debug.o: sequenceDataDiff.cpp sequenceDataDiff.h \ | |
| 270 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 271 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \ | |
| 272 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \ | |
| 273 | ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \ | |
| 274 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h | |
| 275 | suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.debug.o: suffStatComponentJointNoGamma.cpp \ | |
| 276 | suffStatComponentJointNoGamma.h ../../libs/phylogeny/definitions.h |
| 0 | gainLossOptions.o gainLossOptions.debug.o: gainLossOptions.cpp gainLossOptions.h \ | |
| 1 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/errorMsg.h \ | |
| 2 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \ | |
| 3 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/alphabet.h \ | |
| 4 | ../../libs/phylogeny/Parameters.h | |
| 5 | gainLoss.o gainLoss.debug.o: gainLoss.cpp computePosteriorExpectationOfChange.h \ | |
| 6 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/simulateJumps.h \ | |
| 7 | ../../libs/phylogeny/simulateJumpsAbstract.h \ | |
| 8 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 9 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 10 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 11 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 12 | ../../libs/phylogeny/replacementModel.h \ | |
| 13 | ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \ | |
| 14 | ../../libs/phylogeny/computeJumps.h ../../libs/phylogeny/someUtil.h \ | |
| 15 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/sequenceContainer.h \ | |
| 16 | ../../libs/phylogeny/sequence.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 17 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 18 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 19 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 20 | ../../libs/phylogeny/computePijComponent.h \ | |
| 21 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 22 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 23 | ../../libs/phylogeny/generalGammaDistribution.h gainLoss.h \ | |
| 24 | ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \ | |
| 25 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 26 | ../../libs/phylogeny/countTableComponent.h \ | |
| 27 | ../../libs/phylogeny/computePijComponent.h \ | |
| 28 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 29 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 30 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 31 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 32 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 33 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 34 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 35 | ../../libs/phylogeny/distanceTable.h \ | |
| 36 | ../../libs/phylogeny/distanceMethod.h \ | |
| 37 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 38 | ../../libs/phylogeny/errorMsg.h \ | |
| 39 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 40 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 41 | ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \ | |
| 42 | ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \ | |
| 43 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 44 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 45 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 46 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 47 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 48 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 49 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 50 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 51 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 52 | ../../libs/phylogeny/logFile.h \ | |
| 53 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 54 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \ | |
| 55 | ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \ | |
| 56 | ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \ | |
| 57 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 58 | ../../libs/phylogeny/sequence.h \ | |
| 59 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 60 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 61 | ../../libs/phylogeny/jcDistance.h \ | |
| 62 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 63 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 64 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 65 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 66 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 67 | optimizeGainLossModel.h ../../libs/phylogeny/computeUpAlg.h \ | |
| 68 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 69 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 70 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 71 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 72 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 73 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 74 | ../../libs/phylogeny/uniDistribution.h gainLossOptimizer.h \ | |
| 75 | ../../libs/phylogeny/gammaDistributionPlusInvariant.h \ | |
| 76 | ../../libs/phylogeny/simulateTree.h ../../libs/phylogeny/phylipFormat.h \ | |
| 77 | ../../libs/phylogeny/maseFormat.h ../../libs/phylogeny/fastaFormat.h \ | |
| 78 | ../../libs/phylogeny/clustalFormat.h rate4siteGL.h gainLoss4site.h \ | |
| 79 | siteSpecificGL.h computeCountsGL.h computeCorrelations.h \ | |
| 80 | ../../libs/phylogeny/Parameters.h \ | |
| 81 | ../../libs/phylogeny/extremeValDistribution.h simulateOnePos.h \ | |
| 82 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/threeStateModel.h \ | |
| 83 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \ | |
| 84 | ../../libs/phylogeny/oneTwoMoreModel.h sankoffReconstructGL.h bblLS.h \ | |
| 85 | ../../libs/phylogeny/bblEMfixRoot.h | |
| 86 | gainLossUtils.o gainLossUtils.debug.o: gainLossUtils.cpp gainLossUtils.h \ | |
| 87 | ../../libs/phylogeny/definitions.h gainLossAlphabet.h \ | |
| 88 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/errorMsg.h \ | |
| 89 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 90 | ../../libs/phylogeny/definitions.h \ | |
| 91 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 92 | ../../libs/phylogeny/distribution.h ../../libs/phylogeny/errorMsg.h \ | |
| 93 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 94 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 95 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 96 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 97 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 98 | ../../libs/phylogeny/replacementModel.h \ | |
| 99 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 100 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 101 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \ | |
| 102 | ../../libs/phylogeny/gainLossAlphabet.h ../../libs/phylogeny/tree.h \ | |
| 103 | ../../libs/phylogeny/readTree.h \ | |
| 104 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 105 | ../../libs/phylogeny/unObservableData.h \ | |
| 106 | ../../libs/phylogeny/computePijComponent.h \ | |
| 107 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 108 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 109 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 110 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 111 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 112 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 113 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/matrixUtils.h \ | |
| 114 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 115 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 116 | ../../libs/phylogeny/treeIt.h \ | |
| 117 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 118 | ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \ | |
| 119 | gainLossModel.h ../../libs/phylogeny/replacementModel.h \ | |
| 120 | ../../libs/phylogeny/fromQtoPt.h \ | |
| 121 | ../../libs/phylogeny/gammaDistributionPlusInvariant.h \ | |
| 122 | ../../libs/phylogeny/Parameters.h | |
| 123 | optimizeGainLossModel.o optimizeGainLossModel.debug.o: optimizeGainLossModel.cpp \ | |
| 124 | optimizeGainLossModel.h ../../libs/phylogeny/bblEM.h \ | |
| 125 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 126 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 127 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 128 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 129 | ../../libs/phylogeny/replacementModel.h \ | |
| 130 | ../../libs/phylogeny/distribution.h \ | |
| 131 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 132 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 133 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 134 | ../../libs/phylogeny/countTableComponent.h \ | |
| 135 | ../../libs/phylogeny/computePijComponent.h \ | |
| 136 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 137 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 138 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 139 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 140 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 141 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 142 | ../../libs/phylogeny/computePijComponent.h \ | |
| 143 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/definitions.h \ | |
| 144 | gainLossModel.h ../../libs/phylogeny/replacementModel.h \ | |
| 145 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \ | |
| 146 | ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \ | |
| 147 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 148 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 149 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 150 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 151 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 152 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 153 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 154 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 155 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 156 | ../../libs/phylogeny/logFile.h \ | |
| 157 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 158 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 159 | ../../libs/phylogeny/treeIt.h \ | |
| 160 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 161 | ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \ | |
| 162 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 163 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 164 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \ | |
| 165 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 166 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 167 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 168 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/Parameters.h | |
| 169 | optimizeGainLossModelVV.o optimizeGainLossModelVV.debug.o: optimizeGainLossModelVV.cpp \ | |
| 170 | optimizeGainLossModelVV.h ../../libs/phylogeny/bblEM.h \ | |
| 171 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 172 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 173 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 174 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 175 | ../../libs/phylogeny/replacementModel.h \ | |
| 176 | ../../libs/phylogeny/distribution.h \ | |
| 177 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 178 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 179 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 180 | ../../libs/phylogeny/countTableComponent.h \ | |
| 181 | ../../libs/phylogeny/computePijComponent.h \ | |
| 182 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 183 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 184 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 185 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 186 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 187 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 188 | ../../libs/phylogeny/computePijComponent.h \ | |
| 189 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/definitions.h \ | |
| 190 | gainLossModel.h ../../libs/phylogeny/replacementModel.h \ | |
| 191 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \ | |
| 192 | ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \ | |
| 193 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 194 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 195 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 196 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 197 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 198 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 199 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 200 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 201 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 202 | ../../libs/phylogeny/logFile.h \ | |
| 203 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 204 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 205 | ../../libs/phylogeny/treeIt.h \ | |
| 206 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 207 | ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \ | |
| 208 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 209 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 210 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 211 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 212 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \ | |
| 213 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 214 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 215 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 216 | ../../libs/phylogeny/Parameters.h | |
| 217 | likelihoodComputationGL.o likelihoodComputationGL.debug.o: \ | |
| 218 | ../../libs/phylogeny/likelihoodComputationGL.cpp \ | |
| 219 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 220 | ../../libs/phylogeny/definitions.h \ | |
| 221 | ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \ | |
| 222 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 223 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 224 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 225 | ../../libs/phylogeny/replacementModel.h \ | |
| 226 | ../../libs/phylogeny/distribution.h \ | |
| 227 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 228 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 229 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 230 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 231 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 232 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 233 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 234 | ../../libs/phylogeny/unObservableData.h \ | |
| 235 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 236 | ../../libs/phylogeny/likelihoodComputation.h | |
| 237 | gainLossModel.o gainLossModel.debug.o: gainLossModel.cpp gainLossModel.h \ | |
| 238 | ../../libs/phylogeny/definitions.h \ | |
| 239 | ../../libs/phylogeny/replacementModel.h \ | |
| 240 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/fromQtoPt.h \ | |
| 241 | ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/errorMsg.h \ | |
| 242 | ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/logFile.h \ | |
| 243 | ../../libs/phylogeny/errorMsg.h gainLossUtils.h gainLossAlphabet.h \ | |
| 244 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 245 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 246 | ../../libs/phylogeny/distribution.h \ | |
| 247 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 248 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 249 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 250 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 251 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 252 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 253 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 254 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 255 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \ | |
| 256 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 257 | ../../libs/phylogeny/unObservableData.h \ | |
| 258 | ../../libs/phylogeny/computePijComponent.h \ | |
| 259 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 260 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 261 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 262 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 263 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 264 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 265 | ../../libs/phylogeny/logFile.h \ | |
| 266 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 267 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 268 | ../../libs/phylogeny/treeIt.h \ | |
| 269 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 270 | ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h | |
| 271 | siteSpecificGL.o siteSpecificGL.debug.o: siteSpecificGL.cpp siteSpecificGL.h \ | |
| 272 | ../../libs/phylogeny/definitions.h \ | |
| 273 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 274 | ../../libs/phylogeny/definitions.h \ | |
| 275 | ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \ | |
| 276 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 277 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 278 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 279 | ../../libs/phylogeny/replacementModel.h \ | |
| 280 | ../../libs/phylogeny/distribution.h \ | |
| 281 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 282 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 283 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 284 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 285 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 286 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 287 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 288 | ../../libs/phylogeny/unObservableData.h \ | |
| 289 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 290 | ../../libs/phylogeny/numRec.h ../../libs/phylogeny/uniformDistribution.h \ | |
| 291 | ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \ | |
| 292 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 293 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 294 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 295 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 296 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 297 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 298 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 299 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 300 | ../../libs/phylogeny/logFile.h \ | |
| 301 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 302 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 303 | ../../libs/phylogeny/treeIt.h \ | |
| 304 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 305 | ../../libs/phylogeny/trivialAccelerator.h gainLossModel.h \ | |
| 306 | ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \ | |
| 307 | ../../libs/phylogeny/errorMsg.h gainLossOptions.h | |
| 308 | computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.debug.o: \ | |
| 309 | computePosteriorExpectationOfChange.cpp \ | |
| 310 | computePosteriorExpectationOfChange.h ../../libs/phylogeny/definitions.h \ | |
| 311 | ../../libs/phylogeny/simulateJumps.h \ | |
| 312 | ../../libs/phylogeny/simulateJumpsAbstract.h \ | |
| 313 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 314 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 315 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 316 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 317 | ../../libs/phylogeny/replacementModel.h \ | |
| 318 | ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \ | |
| 319 | ../../libs/phylogeny/computeJumps.h ../../libs/phylogeny/someUtil.h \ | |
| 320 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/sequenceContainer.h \ | |
| 321 | ../../libs/phylogeny/sequence.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 322 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 323 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 324 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 325 | ../../libs/phylogeny/computePijComponent.h \ | |
| 326 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 327 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 328 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 329 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 330 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 331 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 332 | ../../libs/phylogeny/computePijComponent.h \ | |
| 333 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/matrixUtils.h \ | |
| 334 | ../../libs/phylogeny/treeIt.h \ | |
| 335 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 336 | ../../libs/phylogeny/unObservableData.h gainLossOptions.h \ | |
| 337 | gainLossModel.h ../../libs/phylogeny/replacementModel.h \ | |
| 338 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \ | |
| 339 | gainLossUtils.h gainLossAlphabet.h \ | |
| 340 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 341 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 342 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 343 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 344 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 345 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 346 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 347 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 348 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 349 | ../../libs/phylogeny/logFile.h \ | |
| 350 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 351 | ../../libs/phylogeny/someUtil.h \ | |
| 352 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 353 | ../../libs/phylogeny/trivialAccelerator.h | |
| 354 | gainLossProject.o gainLossProject.debug.o: gainLossProject.cpp gainLoss.h \ | |
| 355 | ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \ | |
| 356 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/bblEM.h \ | |
| 357 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \ | |
| 358 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \ | |
| 359 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 360 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 361 | ../../libs/phylogeny/distribution.h \ | |
| 362 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 363 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 364 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 365 | ../../libs/phylogeny/countTableComponent.h \ | |
| 366 | ../../libs/phylogeny/computePijComponent.h \ | |
| 367 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 368 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 369 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 370 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 371 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 372 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 373 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 374 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 375 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 376 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 377 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/distanceTable.h \ | |
| 378 | ../../libs/phylogeny/distanceMethod.h \ | |
| 379 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 380 | ../../libs/phylogeny/errorMsg.h \ | |
| 381 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 382 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 383 | ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \ | |
| 384 | ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \ | |
| 385 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 386 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 387 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 388 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 389 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 390 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 391 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 392 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 393 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 394 | ../../libs/phylogeny/logFile.h \ | |
| 395 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 396 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 397 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \ | |
| 398 | gainLossOptions.h ancestralReconstructStates.h \ | |
| 399 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 400 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 401 | ../../libs/phylogeny/sequence.h \ | |
| 402 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 403 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 404 | ../../libs/phylogeny/jcDistance.h \ | |
| 405 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 406 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 407 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 408 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 409 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 410 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 411 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 412 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 413 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 414 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 415 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 416 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 417 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 418 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 419 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 420 | ../../libs/phylogeny/uniDistribution.h \ | |
| 421 | computePosteriorExpectationOfChange.h \ | |
| 422 | ../../libs/phylogeny/simulateJumps.h \ | |
| 423 | ../../libs/phylogeny/simulateJumpsAbstract.h \ | |
| 424 | ../../libs/phylogeny/computeJumps.h \ | |
| 425 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 426 | ../../libs/phylogeny/Parameters.h | |
| 427 | gainLossOptimizer.o gainLossOptimizer.debug.o: gainLossOptimizer.cpp gainLossOptimizer.h \ | |
| 428 | ../../libs/phylogeny/definitions.h \ | |
| 429 | ../../libs/phylogeny/replacementModel.h \ | |
| 430 | ../../libs/phylogeny/definitions.h gainLoss.h \ | |
| 431 | ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \ | |
| 432 | ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \ | |
| 433 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 434 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 435 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 436 | ../../libs/phylogeny/distribution.h \ | |
| 437 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 438 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 439 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 440 | ../../libs/phylogeny/countTableComponent.h \ | |
| 441 | ../../libs/phylogeny/computePijComponent.h \ | |
| 442 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 443 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 444 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 445 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 446 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 447 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 448 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 449 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 450 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 451 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 452 | ../../libs/phylogeny/distanceTable.h \ | |
| 453 | ../../libs/phylogeny/distanceMethod.h \ | |
| 454 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 455 | ../../libs/phylogeny/errorMsg.h \ | |
| 456 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 457 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 458 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \ | |
| 459 | gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 460 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 461 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 462 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 463 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 464 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 465 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 466 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 467 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 468 | ../../libs/phylogeny/logFile.h \ | |
| 469 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 470 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 471 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \ | |
| 472 | gainLossOptions.h ancestralReconstructStates.h \ | |
| 473 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 474 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 475 | ../../libs/phylogeny/sequence.h \ | |
| 476 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 477 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 478 | ../../libs/phylogeny/jcDistance.h \ | |
| 479 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 480 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 481 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 482 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 483 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 484 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 485 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 486 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 487 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 488 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 489 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 490 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 491 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 492 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 493 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 494 | ../../libs/phylogeny/uniDistribution.h \ | |
| 495 | ../../libs/phylogeny/bblEMfixRoot.h bblLS.h | |
| 496 | ancestralReconstructStates.o ancestralReconstructStates.debug.o: ancestralReconstructStates.cpp \ | |
| 497 | ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \ | |
| 498 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \ | |
| 499 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 500 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/suffStatComponent.h \ | |
| 501 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 502 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 503 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 504 | ../../libs/phylogeny/computePijComponent.h \ | |
| 505 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 506 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 507 | ../../libs/phylogeny/replacementModel.h \ | |
| 508 | ../../libs/phylogeny/distribution.h \ | |
| 509 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 510 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 511 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 512 | ../../libs/phylogeny/definitions.h gainLossAlphabet.h \ | |
| 513 | ../../libs/phylogeny/matrixUtils.h \ | |
| 514 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 515 | ../../libs/phylogeny/sequence.h ../../libs/phylogeny/someUtil.h \ | |
| 516 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \ | |
| 517 | ../../libs/phylogeny/logFile.h | |
| 518 | rate4siteGL.o rate4siteGL.debug.o: rate4siteGL.cpp rate4siteGL.h \ | |
| 519 | ../../libs/phylogeny/definitions.h \ | |
| 520 | ../../libs/phylogeny/replacementModel.h \ | |
| 521 | ../../libs/phylogeny/definitions.h gainLoss.h \ | |
| 522 | ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \ | |
| 523 | ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \ | |
| 524 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 525 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 526 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 527 | ../../libs/phylogeny/distribution.h \ | |
| 528 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 529 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 530 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 531 | ../../libs/phylogeny/countTableComponent.h \ | |
| 532 | ../../libs/phylogeny/computePijComponent.h \ | |
| 533 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 534 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 535 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 536 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 537 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 538 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 539 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 540 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 541 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 542 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 543 | ../../libs/phylogeny/distanceTable.h \ | |
| 544 | ../../libs/phylogeny/distanceMethod.h \ | |
| 545 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 546 | ../../libs/phylogeny/errorMsg.h \ | |
| 547 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 548 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 549 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \ | |
| 550 | gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 551 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 552 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 553 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 554 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 555 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 556 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 557 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 558 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 559 | ../../libs/phylogeny/logFile.h \ | |
| 560 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 561 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 562 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \ | |
| 563 | gainLossOptions.h ancestralReconstructStates.h \ | |
| 564 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 565 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 566 | ../../libs/phylogeny/sequence.h \ | |
| 567 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 568 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 569 | ../../libs/phylogeny/jcDistance.h \ | |
| 570 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 571 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 572 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 573 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 574 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 575 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 576 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 577 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 578 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 579 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 580 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 581 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 582 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 583 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 584 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 585 | ../../libs/phylogeny/uniDistribution.h | |
| 586 | computeCountsGL.o computeCountsGL.debug.o: computeCountsGL.cpp computeCountsGL.h \ | |
| 587 | ../../libs/phylogeny/definitions.h \ | |
| 588 | ../../libs/phylogeny/replacementModel.h \ | |
| 589 | ../../libs/phylogeny/definitions.h gainLoss.h \ | |
| 590 | ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \ | |
| 591 | ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \ | |
| 592 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 593 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 594 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 595 | ../../libs/phylogeny/distribution.h \ | |
| 596 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 597 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 598 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 599 | ../../libs/phylogeny/countTableComponent.h \ | |
| 600 | ../../libs/phylogeny/computePijComponent.h \ | |
| 601 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 602 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 603 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 604 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 605 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 606 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 607 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 608 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 609 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 610 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 611 | ../../libs/phylogeny/distanceTable.h \ | |
| 612 | ../../libs/phylogeny/distanceMethod.h \ | |
| 613 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 614 | ../../libs/phylogeny/errorMsg.h \ | |
| 615 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 616 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 617 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \ | |
| 618 | gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 619 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 620 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 621 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 622 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 623 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 624 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 625 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 626 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 627 | ../../libs/phylogeny/logFile.h \ | |
| 628 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 629 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 630 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \ | |
| 631 | gainLossOptions.h ancestralReconstructStates.h \ | |
| 632 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 633 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 634 | ../../libs/phylogeny/sequence.h \ | |
| 635 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 636 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 637 | ../../libs/phylogeny/jcDistance.h \ | |
| 638 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 639 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 640 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 641 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 642 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 643 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 644 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 645 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 646 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 647 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 648 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 649 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 650 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 651 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 652 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 653 | ../../libs/phylogeny/uniDistribution.h \ | |
| 654 | computePosteriorExpectationOfChange.h \ | |
| 655 | ../../libs/phylogeny/simulateJumps.h \ | |
| 656 | ../../libs/phylogeny/simulateJumpsAbstract.h \ | |
| 657 | ../../libs/phylogeny/computeJumps.h \ | |
| 658 | ../../libs/phylogeny/suffStatComponent.h | |
| 659 | computeCorrelations.o computeCorrelations.debug.o: computeCorrelations.cpp computeCorrelations.h \ | |
| 660 | ../../libs/phylogeny/definitions.h \ | |
| 661 | ../../libs/phylogeny/replacementModel.h \ | |
| 662 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/Parameters.h \ | |
| 663 | gainLoss.h ../../libs/phylogeny/aaJC.h \ | |
| 664 | ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/bblEM.h \ | |
| 665 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \ | |
| 666 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \ | |
| 667 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 668 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 669 | ../../libs/phylogeny/distribution.h \ | |
| 670 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 671 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 672 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 673 | ../../libs/phylogeny/countTableComponent.h \ | |
| 674 | ../../libs/phylogeny/computePijComponent.h \ | |
| 675 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 676 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 677 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 678 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 679 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 680 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 681 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 682 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 683 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 684 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 685 | ../../libs/phylogeny/distanceTable.h \ | |
| 686 | ../../libs/phylogeny/distanceMethod.h \ | |
| 687 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 688 | ../../libs/phylogeny/errorMsg.h \ | |
| 689 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 690 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 691 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \ | |
| 692 | gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 693 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 694 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 695 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 696 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 697 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 698 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 699 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 700 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 701 | ../../libs/phylogeny/logFile.h \ | |
| 702 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 703 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 704 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \ | |
| 705 | gainLossOptions.h ancestralReconstructStates.h \ | |
| 706 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 707 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 708 | ../../libs/phylogeny/sequence.h \ | |
| 709 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 710 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 711 | ../../libs/phylogeny/jcDistance.h \ | |
| 712 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 713 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 714 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 715 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 716 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 717 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 718 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 719 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 720 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 721 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 722 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 723 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 724 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 725 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 726 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 727 | ../../libs/phylogeny/uniDistribution.h \ | |
| 728 | ../../libs/phylogeny/extremeValDistribution.h | |
| 729 | gainLoss4site.o gainLoss4site.debug.o: gainLoss4site.cpp gainLoss4site.h \ | |
| 730 | ../../libs/phylogeny/definitions.h \ | |
| 731 | ../../libs/phylogeny/replacementModel.h \ | |
| 732 | ../../libs/phylogeny/definitions.h gainLoss.h \ | |
| 733 | ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \ | |
| 734 | ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \ | |
| 735 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 736 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 737 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 738 | ../../libs/phylogeny/distribution.h \ | |
| 739 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 740 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 741 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 742 | ../../libs/phylogeny/countTableComponent.h \ | |
| 743 | ../../libs/phylogeny/computePijComponent.h \ | |
| 744 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 745 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 746 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 747 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 748 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 749 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 750 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 751 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 752 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 753 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 754 | ../../libs/phylogeny/distanceTable.h \ | |
| 755 | ../../libs/phylogeny/distanceMethod.h \ | |
| 756 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 757 | ../../libs/phylogeny/errorMsg.h \ | |
| 758 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 759 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 760 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \ | |
| 761 | gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 762 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 763 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 764 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 765 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 766 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 767 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 768 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 769 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 770 | ../../libs/phylogeny/logFile.h \ | |
| 771 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 772 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \ | |
| 773 | ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \ | |
| 774 | gainLossOptions.h ancestralReconstructStates.h \ | |
| 775 | ../../libs/phylogeny/computeDownAlg.h \ | |
| 776 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 777 | ../../libs/phylogeny/sequence.h \ | |
| 778 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 779 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 780 | ../../libs/phylogeny/jcDistance.h \ | |
| 781 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 782 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 783 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 784 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 785 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 786 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 787 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 788 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 789 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 790 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \ | |
| 791 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 792 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 793 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 794 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 795 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 796 | ../../libs/phylogeny/uniDistribution.h siteSpecificGL.h | |
| 797 | simulateChangesAlongTree.o simulateChangesAlongTree.debug.o: simulateChangesAlongTree.cpp \ | |
| 798 | simulateChangesAlongTree.h ../../libs/phylogeny/definitions.h \ | |
| 799 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \ | |
| 800 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 801 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 802 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 803 | ../../libs/phylogeny/replacementModel.h \ | |
| 804 | ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \ | |
| 805 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 806 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 807 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 808 | ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/matrixUtils.h \ | |
| 809 | gainLoss.h ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \ | |
| 810 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/stochasticProcess.h \ | |
| 811 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 812 | ../../libs/phylogeny/countTableComponent.h \ | |
| 813 | ../../libs/phylogeny/computePijComponent.h \ | |
| 814 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 815 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 816 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 817 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 818 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 819 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 820 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 821 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 822 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 823 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 824 | ../../libs/phylogeny/distanceTable.h \ | |
| 825 | ../../libs/phylogeny/distanceMethod.h \ | |
| 826 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 827 | ../../libs/phylogeny/errorMsg.h \ | |
| 828 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 829 | ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \ | |
| 830 | ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \ | |
| 831 | gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 832 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 833 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 834 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 835 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 836 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 837 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 838 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 839 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 840 | ../../libs/phylogeny/logFile.h \ | |
| 841 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 842 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \ | |
| 843 | ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \ | |
| 844 | ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \ | |
| 845 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 846 | ../../libs/phylogeny/sequence.h \ | |
| 847 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 848 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 849 | ../../libs/phylogeny/jcDistance.h \ | |
| 850 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 851 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 852 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 853 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 854 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 855 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 856 | ../../libs/phylogeny/computeUpAlg.h \ | |
| 857 | ../../libs/phylogeny/unObservableData.h \ | |
| 858 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 859 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 860 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 861 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 862 | ../../libs/phylogeny/siteSpecificRate.h \ | |
| 863 | ../../libs/phylogeny/uniDistribution.h | |
| 864 | simulateOnePos.o simulateOnePos.debug.o: simulateOnePos.cpp ../../libs/phylogeny/definitions.h \ | |
| 865 | simulateOnePos.h ../../libs/phylogeny/tree.h \ | |
| 866 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/readTree.h \ | |
| 867 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \ | |
| 868 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 869 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 870 | ../../libs/phylogeny/replacementModel.h \ | |
| 871 | ../../libs/phylogeny/distribution.h \ | |
| 872 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 873 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \ | |
| 874 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 875 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/threeStateModel.h \ | |
| 876 | ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \ | |
| 877 | ../../libs/phylogeny/oneTwoMoreModel.h \ | |
| 878 | ../../libs/phylogeny/simulateTree.h ../../libs/phylogeny/tree.h \ | |
| 879 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 880 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 881 | ../../libs/phylogeny/threeStateAlphabet.h \ | |
| 882 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 883 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 884 | ../../libs/phylogeny/trivialAccelerator.h \ | |
| 885 | ../../libs/phylogeny/uniDistribution.h ../../libs/phylogeny/sequence.h \ | |
| 886 | simulateChangesAlongTree.h ../../libs/phylogeny/treeIt.h \ | |
| 887 | ../../libs/phylogeny/fastaFormat.h gainLoss.h \ | |
| 888 | ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \ | |
| 889 | ../../libs/phylogeny/countTableComponent.h \ | |
| 890 | ../../libs/phylogeny/computePijComponent.h \ | |
| 891 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 892 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 893 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 894 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 895 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \ | |
| 896 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 897 | ../../libs/phylogeny/chebyshevAccelerator.h \ | |
| 898 | ../../libs/phylogeny/checkcovFanctors.h \ | |
| 899 | ../../libs/phylogeny/checkcovFanctorsWithFactors.h \ | |
| 900 | ../../libs/phylogeny/likelihoodComputationFactors.h \ | |
| 901 | ../../libs/phylogeny/distanceTable.h \ | |
| 902 | ../../libs/phylogeny/distanceMethod.h \ | |
| 903 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 904 | ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/fastStartTree.h \ | |
| 905 | gainLossAlphabet.h gainLossModel.h \ | |
| 906 | ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \ | |
| 907 | ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \ | |
| 908 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 909 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 910 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 911 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 912 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 913 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 914 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 915 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 916 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 917 | ../../libs/phylogeny/logFile.h \ | |
| 918 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 919 | ../../libs/phylogeny/someUtil.h gainLossOptions.h \ | |
| 920 | ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \ | |
| 921 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 922 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 923 | ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \ | |
| 924 | ../../libs/phylogeny/jcDistance.h \ | |
| 925 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 926 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 927 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \ | |
| 928 | ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \ | |
| 929 | ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \ | |
| 930 | optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \ | |
| 931 | ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/talRandom.h \ | |
| 932 | ../../libs/phylogeny/unObservableData.h \ | |
| 933 | ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \ | |
| 934 | ../../libs/phylogeny/readDatMatrix.h \ | |
| 935 | ../../libs/phylogeny/datMatrixHolder.h \ | |
| 936 | ../../libs/phylogeny/siteSpecificRate.h | |
| 937 | bblLS.o bblLS.debug.o: bblLS.cpp bblLS.h ../../libs/phylogeny/definitions.h \ | |
| 938 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \ | |
| 939 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 940 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/sequenceContainer.h \ | |
| 941 | ../../libs/phylogeny/sequence.h ../../libs/phylogeny/alphabet.h \ | |
| 942 | ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \ | |
| 943 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 944 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 945 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 946 | ../../libs/phylogeny/replacementModel.h \ | |
| 947 | ../../libs/phylogeny/distribution.h \ | |
| 948 | ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/tree.h \ | |
| 949 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 950 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 951 | ../../libs/phylogeny/computePijComponent.h \ | |
| 952 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 953 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 954 | ../../libs/phylogeny/generalGammaDistribution.h gainLossUtils.h \ | |
| 955 | gainLossAlphabet.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 956 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 957 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 958 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 959 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 960 | ../../libs/phylogeny/unObservableData.h \ | |
| 961 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 962 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 963 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 964 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 965 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/matrixUtils.h \ | |
| 966 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 967 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \ | |
| 968 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 969 | ../../libs/phylogeny/trivialAccelerator.h ../../libs/phylogeny/numRec.h \ | |
| 970 | ../../libs/phylogeny/likelihoodComputation.h \ | |
| 971 | ../../libs/phylogeny/suffStatComponent.h \ | |
| 972 | ../../libs/phylogeny/likelihoodComputationGL.h \ | |
| 973 | ../../libs/phylogeny/computeUpAlg.h gainLossOptions.h | |
| 974 | sankoffReconstructGL.o sankoffReconstructGL.debug.o: sankoffReconstructGL.cpp sankoffReconstructGL.h \ | |
| 975 | ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \ | |
| 976 | ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \ | |
| 977 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/logFile.h \ | |
| 978 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/alphabet.h \ | |
| 979 | ../../libs/phylogeny/definitions.h \ | |
| 980 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 981 | ../../libs/phylogeny/pijAccelerator.h \ | |
| 982 | ../../libs/phylogeny/replacementModel.h \ | |
| 983 | ../../libs/phylogeny/distribution.h \ | |
| 984 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 985 | ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \ | |
| 986 | ../../libs/phylogeny/gainLossAlphabet.h gainLossUtils.h \ | |
| 987 | gainLossAlphabet.h ../../libs/phylogeny/gammaDistribution.h \ | |
| 988 | ../../libs/phylogeny/generalGammaDistribution.h \ | |
| 989 | ../../libs/phylogeny/gammaDistributionFixedCategories.h \ | |
| 990 | ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \ | |
| 991 | ../../libs/phylogeny/GamMixtureOptimizer.h \ | |
| 992 | ../../libs/phylogeny/stochasticProcess.h \ | |
| 993 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/tree.h \ | |
| 994 | ../../libs/phylogeny/mixtureDistribution.h \ | |
| 995 | ../../libs/phylogeny/unObservableData.h \ | |
| 996 | ../../libs/phylogeny/computePijComponent.h \ | |
| 997 | ../../libs/phylogeny/multipleStochasticProcess.h \ | |
| 998 | ../../libs/phylogeny/gammaDistribution.h \ | |
| 999 | ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \ | |
| 1000 | ../../libs/phylogeny/distributionPlusInvariant.h \ | |
| 1001 | ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \ | |
| 1002 | ../../libs/phylogeny/uniformDistribution.h \ | |
| 1003 | ../../libs/phylogeny/matrixUtils.h \ | |
| 1004 | ../../libs/phylogeny/mixtureDistribution.h ../../libs/phylogeny/treeIt.h \ | |
| 1005 | ../../libs/phylogeny/evaluateCharacterFreq.h \ | |
| 1006 | ../../libs/phylogeny/trivialAccelerator.h \ | |
| 1007 | ../../libs/phylogeny/threeStateAlphabet.h \ | |
| 1008 | ../../libs/phylogeny/sequence.h ../../libs/phylogeny/recognizeFormat.h \ | |
| 1009 | ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \ | |
| 1010 | ../../libs/phylogeny/treeUtil.h ../../libs/phylogeny/amino.h \ | |
| 1011 | ../../libs/phylogeny/geneticCodeHolder.h ../../libs/phylogeny/codon.h \ | |
| 1012 | ../../libs/phylogeny/nucleotide.h ../../libs/phylogeny/integerAlphabet.h \ | |
| 1013 | gainLossOptions.h |
| 0 | indelCoder.o indelCoder.debug.o: indelCoder.cpp indelCoder.h gaps.h \ | |
| 1 | ../../libs/phylogeny/definitions.h character.h \ | |
| 2 | ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \ | |
| 3 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \ | |
| 4 | indelCoderOptions.h ../../libs/phylogeny/amino.h \ | |
| 5 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \ | |
| 6 | ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \ | |
| 7 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 8 | ../../libs/phylogeny/mulAlphabet.h \ | |
| 9 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 10 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 11 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \ | |
| 12 | ../../libs/phylogeny/talRandom.h indelCoderUtils.h | |
| 13 | indelCoderOptions.o indelCoderOptions.debug.o: indelCoderOptions.cpp indelCoderOptions.h \ | |
| 14 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/errorMsg.h \ | |
| 15 | ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \ | |
| 16 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/alphabet.h \ | |
| 17 | ../../libs/phylogeny/Parameters.h | |
| 18 | indelCoderProject.o indelCoderProject.debug.o: indelCoderProject.cpp indelCoder.h gaps.h \ | |
| 19 | ../../libs/phylogeny/definitions.h character.h \ | |
| 20 | ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \ | |
| 21 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \ | |
| 22 | indelCoderOptions.h ../../libs/phylogeny/amino.h \ | |
| 23 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \ | |
| 24 | ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \ | |
| 25 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 26 | ../../libs/phylogeny/mulAlphabet.h \ | |
| 27 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 28 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 29 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \ | |
| 30 | ../../libs/phylogeny/talRandom.h indelCoderUtils.h \ | |
| 31 | ../../libs/phylogeny/Parameters.h | |
| 32 | indelCoderUtils.o indelCoderUtils.debug.o: indelCoderUtils.cpp indelCoderUtils.h \ | |
| 33 | ../../libs/phylogeny/logFile.h indelCoder.h gaps.h \ | |
| 34 | ../../libs/phylogeny/definitions.h character.h \ | |
| 35 | ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \ | |
| 36 | ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \ | |
| 37 | indelCoderOptions.h ../../libs/phylogeny/amino.h \ | |
| 38 | ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \ | |
| 39 | ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \ | |
| 40 | ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \ | |
| 41 | ../../libs/phylogeny/mulAlphabet.h \ | |
| 42 | ../../libs/phylogeny/gainLossAlphabet.h \ | |
| 43 | ../../libs/phylogeny/recognizeFormat.h \ | |
| 44 | ../../libs/phylogeny/sequenceContainer.h \ | |
| 45 | ../../libs/phylogeny/talRandom.h | |
| 46 | character.o character.debug.o: character.cpp character.h ../../libs/phylogeny/definitions.h \ | |
| 47 | gaps.h ../../libs/phylogeny/matrixUtils.h \ | |
| 48 | ../../libs/phylogeny/definitions.h ../../libs/phylogeny/logFile.h \ | |
| 49 | ../../libs/phylogeny/errorMsg.h indelCoderOptions.h | |
| 50 | gaps.o gaps.debug.o: gaps.cpp gaps.h ../../libs/phylogeny/definitions.h |