mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:20:25 +08:00
1239 lines
26 KiB
XML
1239 lines
26 KiB
XML
<?xml version="1.0" encoding="windows-1255"?>
|
|
<VisualStudioProject
|
|
ProjectType="Visual C++"
|
|
Version="7.10"
|
|
Name="phylogenyLib"
|
|
ProjectGUID="{BEB52DB0-2B2A-41F0-BB49-9EC9817ACBEE}"
|
|
Keyword="Win32Proj">
|
|
<Platforms>
|
|
<Platform
|
|
Name="Win32"/>
|
|
</Platforms>
|
|
<Configurations>
|
|
<Configuration
|
|
Name="Debug|Win32"
|
|
OutputDirectory="Debug"
|
|
IntermediateDirectory="Debug"
|
|
ConfigurationType="4"
|
|
CharacterSet="2">
|
|
<Tool
|
|
Name="VCCLCompilerTool"
|
|
Optimization="0"
|
|
PreprocessorDefinitions="WIN32;_DEBUG;_LIB"
|
|
MinimalRebuild="TRUE"
|
|
BasicRuntimeChecks="3"
|
|
RuntimeLibrary="5"
|
|
RuntimeTypeInfo="TRUE"
|
|
UsePrecompiledHeader="0"
|
|
WarningLevel="3"
|
|
Detect64BitPortabilityProblems="TRUE"
|
|
DebugInformationFormat="4"/>
|
|
<Tool
|
|
Name="VCCustomBuildTool"/>
|
|
<Tool
|
|
Name="VCLibrarianTool"
|
|
OutputFile="$(OutDir)/phylogeny.lib"/>
|
|
<Tool
|
|
Name="VCMIDLTool"/>
|
|
<Tool
|
|
Name="VCPostBuildEventTool"/>
|
|
<Tool
|
|
Name="VCPreBuildEventTool"/>
|
|
<Tool
|
|
Name="VCPreLinkEventTool"/>
|
|
<Tool
|
|
Name="VCResourceCompilerTool"/>
|
|
<Tool
|
|
Name="VCWebServiceProxyGeneratorTool"/>
|
|
<Tool
|
|
Name="VCXMLDataGeneratorTool"/>
|
|
<Tool
|
|
Name="VCManagedWrapperGeneratorTool"/>
|
|
<Tool
|
|
Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
|
|
</Configuration>
|
|
<Configuration
|
|
Name="Release|Win32"
|
|
OutputDirectory="Release"
|
|
IntermediateDirectory="Release"
|
|
ConfigurationType="4"
|
|
CharacterSet="2">
|
|
<Tool
|
|
Name="VCCLCompilerTool"
|
|
PreprocessorDefinitions="WIN32;NDEBUG;_LIB"
|
|
RuntimeLibrary="4"
|
|
RuntimeTypeInfo="TRUE"
|
|
UsePrecompiledHeader="0"
|
|
WarningLevel="3"
|
|
Detect64BitPortabilityProblems="TRUE"
|
|
DebugInformationFormat="3"/>
|
|
<Tool
|
|
Name="VCCustomBuildTool"/>
|
|
<Tool
|
|
Name="VCLibrarianTool"
|
|
OutputFile="$(OutDir)/phylogeny.lib"/>
|
|
<Tool
|
|
Name="VCMIDLTool"/>
|
|
<Tool
|
|
Name="VCPostBuildEventTool"/>
|
|
<Tool
|
|
Name="VCPreBuildEventTool"/>
|
|
<Tool
|
|
Name="VCPreLinkEventTool"/>
|
|
<Tool
|
|
Name="VCResourceCompilerTool"/>
|
|
<Tool
|
|
Name="VCWebServiceProxyGeneratorTool"/>
|
|
<Tool
|
|
Name="VCXMLDataGeneratorTool"/>
|
|
<Tool
|
|
Name="VCManagedWrapperGeneratorTool"/>
|
|
<Tool
|
|
Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
|
|
</Configuration>
|
|
</Configurations>
|
|
<References>
|
|
</References>
|
|
<Files>
|
|
<Filter
|
|
Name="matrices"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\adrianCodon.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\cpREV45.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\dayhoff.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\HIVb.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\HIVw.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\jones.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\LG.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\mtREV24.dat.q">
|
|
</File>
|
|
<File
|
|
RelativePath=".\wag.dat.q">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="alphabet"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\alphabet.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\alphabet.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\amino.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\amino.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\codon.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\codon.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gainLossAlphabet.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gainLossAlphabet.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\geneticCodeHolder.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\geneticCodeHolder.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\indel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\indel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\integerAlphabet.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\integerAlphabet.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\mulAlphabet.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\mulAlphabet.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nucleotide.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nucleotide.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\oneTwoMoreModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\oneTwoMoreModel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\threeStateAlphabet.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\threeStateAlphabet.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="sequence-related"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\evaluateCharacterFreq.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\evaluateCharacterFreq.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\samplingSequences.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\samplingSequences.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\seqContainerTreeMap.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\seqContainerTreeMap.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\seqeuncesFilter.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\seqeuncesFilter.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\sequence.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\sequence.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\sequenceContainer.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\sequenceContainer.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="distribution"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\betaDistribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaDistribution.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaDistributionFixedCategories.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaDistributionFixedCategories.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaDistributionFixedCategoriesWithOmegaUniform.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaDistributionFixedCategoriesWithOmegaUniform.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaOmegaDistribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaOmegaDistribution.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaUtilities.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\betaUtilities.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distribution.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distributionPlusCategory.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distributionPlusCategory.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distributionPlusInvariant.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distributionPlusInvariant.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistribution.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistributionFixedCategories.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistributionFixedCategories.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistributionLaguerre.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistributionLaguerre.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistributionPlusInvariant.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaDistributionPlusInvariant.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaUtilities.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gammaUtilities.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\GamMixtureOptimizer.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\GamMixtureOptimizer.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistribution.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistributionFixedCategories.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistributionFixedCategories.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistributionLaguerre.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistributionLaguerre.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistributionPlusInvariant.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\generalGammaDistributionPlusInvariant.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\mixtureDistribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\mixtureDistribution.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\optGammaMixtureEM.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\optGammaMixtureEM.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\optGammaMixtureLS.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\optGammaMixtureLS.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\suffStatGammaMixture.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\suffStatGammaMixture.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\uniDistribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\uniDistribution.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\uniformDistribution.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\uniformDistribution.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="stochastic&model-stuff"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\datMatrixHolder.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\datMatrixHolder.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromQtoPt.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromQtoPt.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\granthamChemicalDistances.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\granthamChemicalDistances.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\readDatMatrix.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\readDatMatrix.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\ussrvModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\ussrvModel.h">
|
|
</File>
|
|
<Filter
|
|
Name="Accelerator"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\alphaTrivialAccelerator.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\chebyshevAccelerator.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\chebyshevAccelerator.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\pijAccelerator.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\pijAccelerator.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\trivialAccelerator.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="ReplacementModel"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\aaJC.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\aaJC.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\codonJC.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\codonJC.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\goldmanYangModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\goldmanYangModel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gtrModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\gtrModel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\hky.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\hky.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\indelModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\indelModel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nucJC.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nucJC.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\replacementModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\replacementModel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\replacementModelSSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\replacementModelSSRV.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\tamura92.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\tamura92.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\threeStateModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\threeStateModel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\wYangModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\wYangModel.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="StochasticProcess"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\multipleStochasticProcess.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\multipleStochasticProcess.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\stochasticProcess.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\stochasticProcess.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\stochasticProcessSSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\stochasticProcessSSRV.h">
|
|
</File>
|
|
</Filter>
|
|
</Filter>
|
|
<Filter
|
|
Name="Tree-related"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\allTrees.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\allTrees.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\allTreesSeparateModel.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\allTreesSeparateModel.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bootstrap.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bootstrap.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fastStartTree.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fastStartTree.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\readTree.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\readTree.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateTree.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateTree.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\tree.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\tree.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\treeInference.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\treeInference.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\treeIt.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\treeIt.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\treeUtil.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\treeUtil.h">
|
|
</File>
|
|
<Filter
|
|
Name="NNI"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\Nni.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\Nni.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\NNiProp.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\NNiProp.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\NNiSep.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\NNiSep.h">
|
|
</File>
|
|
</Filter>
|
|
</Filter>
|
|
<Filter
|
|
Name="Formats"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\clustalFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\clustalFormat.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fastaFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fastaFormat.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\maseFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\maseFormat.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\molphyFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\molphyFormat.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nexusFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nexusFormat.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\phylipFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\phylipFormat.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\phylipSequentialFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\phylipSequentialFormat.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\recognizeFormat.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\recognizeFormat.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="Likelihood"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\computeDownAlg.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeDownAlg.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeMarginalAlg.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeMarginalAlg.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computePijComponent.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computePijComponent.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeUpAlg.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeUpAlg.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeUpAlgFactors.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDist2Codon.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDist2Codon.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputation.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputation.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputation2Codon.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputation2Codon.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputation2USSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputation2USSRV.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputationFactors.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputationFactors.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputationGL.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likelihoodComputationGL.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\suffStatComponent.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\suffStatComponent.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="Optimization"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\bblEM.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEM.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEM2codon.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEM2codon.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEM2USSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEM2USSRV.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMfixRoot.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMfixRoot.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMProportional.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMProportionalEB.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMProportionalEB.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMProprtional.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMSeperate.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bblEMSeperate.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlpha.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlpha.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlphaAndK.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlphaAndK.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlphaAndNu.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlphaAndNu.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlphaManyTrees.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestAlphaManyTrees.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestGtrModelParams.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestGtrModelParams.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestHKYparam.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestHKYparam.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestParamUSSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestParamUSSRV.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestTamura92param.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\bestTamura92param.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\C_evalParamUSSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\C_evalParamUSSRV.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeCounts.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeCounts.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\countTableComponent.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\countTableComponent.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistance2Codon.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistance2Codon.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistancefixRoot.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistancefixRoot.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="Splits"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\getRandomWeights.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\getRandomWeights.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\split.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\split.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\splitMap.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\splitMap.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\splitTreeUtil.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\splitTreeUtil.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="distance-methods"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\distanceBasedSeqs2Tree.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distanceBasedSeqs2Tree.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distanceMethod.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distances2Tree.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distanceTable.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\distanceTable.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistance.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistance.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistance2USSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistance2USSRV.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistanceProp.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistanceProp.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistancePropEB.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromCountTableComponentToDistancePropEB.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\givenRatesMLDistance.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\givenRatesMLDistance.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\jcDistance.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDist.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDist.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDist2USSRV.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDist2USSRV.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDistfixRoot.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDistfixRoot.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDistProp.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDistProp.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDistPropEB.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\likeDistPropEB.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nj.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\nj.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\njConstrain.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\njConstrain.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\pairwiseGammaDistance.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\pairwiseGammaDistance.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\pDistance.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\posteriorDistance.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\posteriorDistance.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\ssrvDistanceSeqs2Tree.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\ssrvDistanceSeqs2Tree.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="Utils-stuff"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\AddLog.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\AddLog.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\codonUtils.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\codonUtils.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computePosteriorExpectationOfSubstitutions.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computePosteriorExpectationOfSubstitutions.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computePosteriorExpectationOfSubstitutions_nonReversibleSp.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeSubstitutionCounts.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeSubstitutionCounts.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\ConversionUtils.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\ConversionUtils.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\definitions.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\errorMsg.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\errorMsg.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromInstructionFile.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\fromInstructionFile.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\getopt.c">
|
|
</File>
|
|
<File
|
|
RelativePath=".\getopt.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\getopt1.c">
|
|
</File>
|
|
<File
|
|
RelativePath=".\logFile.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\logFile.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\matrixUtils.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\matrixUtils.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\normalDist.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\normalDist.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\numRec.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\numRec.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateCodonsJumps.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateCodonsJumps.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateJumps.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateJumps.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateJumpsAbstract.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateJumpsAbstract.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateRateShiftJumps.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\simulateRateShiftJumps.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\someUtil.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\someUtil.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\talRandom.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\talRandom.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="Rates"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\siteSpecificRate.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\siteSpecificRate.h">
|
|
</File>
|
|
</Filter>
|
|
<Filter
|
|
Name="Misc"
|
|
Filter="">
|
|
<File
|
|
RelativePath=".\checkcovFanctors.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\checkcovFanctorsWithFactors.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\cmdline2EvolObjs.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\cmdline2EvolObjs.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\cmdline2EvolObjs.separate_template_classes.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\createSPFromArgsInfo.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\doubleRep.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\doubleRep.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\findRateOfGene.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\findRateOfGene.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\GLaguer.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\GLaguer.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\khTest.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\khTest.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\logRep.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\logRep.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\Parameters.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\Parameters.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\searchStatus.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\searchStatus.h">
|
|
</File>
|
|
</Filter>
|
|
<File
|
|
RelativePath=".\computeJumps.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\computeJumps.h">
|
|
</File>
|
|
<File
|
|
RelativePath=".\Makefile">
|
|
</File>
|
|
<File
|
|
RelativePath=".\unObservableData.cpp">
|
|
</File>
|
|
<File
|
|
RelativePath=".\unObservableData.h">
|
|
</File>
|
|
</Files>
|
|
<Globals>
|
|
</Globals>
|
|
</VisualStudioProject>
|