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