MANIFEST.in
README.md
setup.py
cpp/AddLog.cpp
cpp/AddLog.h
cpp/CMakeLists.txt
cpp/C_evalParamSSRV.cpp
cpp/C_evalParamSSRV.h
cpp/GLaguer.cpp
cpp/GLaguer.h
cpp/Makefile
cpp/Makefile_slow
cpp/NNiProp.cpp
cpp/NNiProp.h
cpp/NNiSep.cpp
cpp/NNiSep.h
cpp/Nni.cpp
cpp/Nni.h
cpp/TheTree.txt
cpp/aaJC.cpp
cpp/aaJC.h
cpp/allTrees.cpp
cpp/allTrees.h
cpp/allTreesSeparateModel.cpp
cpp/allTreesSeparateModel.h
cpp/alphaTrivialAccelerator.h
cpp/alphabet.cpp
cpp/alphabet.h
cpp/amino.cpp
cpp/amino.h
cpp/bblEM.cpp
cpp/bblEM.h
cpp/bblEM2USSRV.cpp
cpp/bblEM2USSRV.h
cpp/bblEMProportional.h
cpp/bblEMProprtional.cpp
cpp/bblEMSeperate.cpp
cpp/bblEMSeperate.h
cpp/bestAlpha.cpp
cpp/bestAlpha.h
cpp/bestAlphaAndNu.cpp
cpp/bestAlphaAndNu.h
cpp/bestAlphaManyTrees.cpp
cpp/bestAlphaManyTrees.h
cpp/bestHKYparam.cpp
cpp/bestHKYparam.h
cpp/bestParamUSSRV.cpp
cpp/bestParamUSSRV.h
cpp/betaDistribution.cpp
cpp/betaDistribution.h
cpp/betaOmegaDistribution.cpp
cpp/betaOmegaDistribution.h
cpp/betaUtilities.cpp
cpp/betaUtilities.h
cpp/bootstrap.cpp
cpp/bootstrap.h
cpp/chebyshevAccelerator.cpp
cpp/chebyshevAccelerator.h
cpp/checkcovFanctors.h
cpp/checkcovFanctorsWithFactors.h
cpp/clustalFormat.cpp
cpp/clustalFormat.h
cpp/codon.cpp
cpp/codon.h
cpp/codonJC.cpp
cpp/codonJC.h
cpp/computeCounts.cpp
cpp/computeCounts.h
cpp/computeDownAlg.cpp
cpp/computeDownAlg.h
cpp/computeMarginalAlg.cpp
cpp/computeMarginalAlg.h
cpp/computePijComponent.cpp
cpp/computePijComponent.h
cpp/computeUpAlg.cpp
cpp/computeUpAlg.h
cpp/computeUpAlgFactors.cpp
cpp/countTableComponent.cpp
cpp/countTableComponent.h
cpp/cpREV45.dat.q
cpp/datMatrixHolder.cpp
cpp/datMatrixHolder.h
cpp/dayhoff.dat.q
cpp/definitions.h
cpp/distanceBasedSeqs2Tree.cpp
cpp/distanceBasedSeqs2Tree.h
cpp/distanceMethod.h
cpp/distanceTable.cpp
cpp/distanceTable.h
cpp/distances2Tree.h
cpp/distribution.cpp
cpp/distribution.h
cpp/doubleRep.cpp
cpp/doubleRep.h
cpp/errorMsg.cpp
cpp/errorMsg.h
cpp/evaluateCharacterFreq.cpp
cpp/evaluateCharacterFreq.h
cpp/evolObjs.args
cpp/evolObjs.header
cpp/fastStartTree.cpp
cpp/fastStartTree.h
cpp/fastaFormat.cpp
cpp/fastaFormat.h
cpp/findRateOfGene.cpp
cpp/findRateOfGene.h
cpp/fromCountTableComponentToDistance.cpp
cpp/fromCountTableComponentToDistance.h
cpp/fromCountTableComponentToDistance2USSRV.cpp
cpp/fromCountTableComponentToDistance2USSRV.h
cpp/fromCountTableComponentToDistanceProp.cpp
cpp/fromCountTableComponentToDistanceProp.h
cpp/fromInstructionFile.cpp
cpp/fromInstructionFile.h
cpp/fromQtoPt.cpp
cpp/fromQtoPt.h
cpp/gammaDistribution.cpp
cpp/gammaDistribution.h
cpp/gammaUtilities.cpp
cpp/gammaUtilities.h
cpp/generalGammaDistribution.cpp
cpp/generalGammaDistribution.h
cpp/generalGammaDistributionLaguerre.cpp
cpp/generalGammaDistributionLaguerre.h
cpp/geneticCodeHolder.cpp
cpp/geneticCodeHolder.h
cpp/getRandomWeights.cpp
cpp/getRandomWeights.h
cpp/givenRatesMLDistance.cpp
cpp/givenRatesMLDistance.h
cpp/goldmanYangModel.cpp
cpp/goldmanYangModel.h
cpp/granthamChemicalDistances.cpp
cpp/granthamChemicalDistances.h
cpp/hky.cpp
cpp/hky.h
cpp/indel.cpp
cpp/indel.h
cpp/indelModel.cpp
cpp/indelModel.h
cpp/jcDistance.h
cpp/jones.dat.q
cpp/khTest.cpp
cpp/khTest.h
cpp/knownBugs
cpp/likeDist.cpp
cpp/likeDist.h
cpp/likeDist2USSRV.cpp
cpp/likeDist2USSRV.h
cpp/likeDistProp.cpp
cpp/likeDistProp.h
cpp/likelihoodComputation.cpp
cpp/likelihoodComputation.h
cpp/likelihoodComputation2USSRV.cpp
cpp/likelihoodComputation2USSRV.h
cpp/likelihoodComputationFactors.cpp
cpp/likelihoodComputationFactors.h
cpp/logFile.cpp
cpp/logFile.h
cpp/main.cpp
cpp/maseFormat.cpp
cpp/maseFormat.h
cpp/molphyFormat.cpp
cpp/molphyFormat.h
cpp/mtREV24.dat.q
cpp/mulAlphabet.cpp
cpp/mulAlphabet.h
cpp/nexusFormat.cpp
cpp/nexusFormat.h
cpp/nj.cpp
cpp/nj.h
cpp/njConstrain.cpp
cpp/njConstrain.h
cpp/normalDist.cpp
cpp/normalDist.h
cpp/nucJC.cpp
cpp/nucJC.h
cpp/nucleotide.cpp
cpp/nucleotide.h
cpp/numRec.cpp
cpp/numRec.h
cpp/pDistance.h
cpp/pairwiseGammaDistance.cpp
cpp/pairwiseGammaDistance.h
cpp/phylipFormat.cpp
cpp/phylipFormat.h
cpp/pijAccelerator.cpp
cpp/pijAccelerator.h
cpp/posteriorDistance.cpp
cpp/posteriorDistance.h
cpp/r4s.res
cpp/r4sOrig.res
cpp/rate4site.cpp
cpp/rate4site.h
cpp/rate4siteOptions.cpp
cpp/rate4siteOptions.h
cpp/readDatMatrix.cpp
cpp/readDatMatrix.h
cpp/readTree.cpp
cpp/readTree.h
cpp/recognizeFormat.cpp
cpp/recognizeFormat.h
cpp/replacementModel.cpp
cpp/replacementModel.h
cpp/replacementModelSSRV.cpp
cpp/replacementModelSSRV.h
cpp/searchStatus.cpp
cpp/searchStatus.h
cpp/seqContainerTreeMap.cpp
cpp/seqContainerTreeMap.h
cpp/sequence.cpp
cpp/sequence.h
cpp/sequenceContainer.cpp
cpp/sequenceContainer.h
cpp/simulateTree.cpp
cpp/simulateTree.h
cpp/siteSpecificRate.cpp
cpp/siteSpecificRate.h
cpp/someUtil.cpp
cpp/someUtil.h
cpp/split.cpp
cpp/split.h
cpp/splitMap.cpp
cpp/splitMap.h
cpp/splitTreeUtil.cpp
cpp/splitTreeUtil.h
cpp/stochasticProcess.cpp
cpp/stochasticProcess.h
cpp/stochasticProcessSSRV.cpp
cpp/stochasticProcessSSRV.h
cpp/suffStatComponent.cpp
cpp/suffStatComponent.h
cpp/talRandom.cpp
cpp/talRandom.h
cpp/test.msa
cpp/tree.cpp
cpp/tree.h
cpp/treeInference.cpp
cpp/treeInference.h
cpp/treeIt.cpp
cpp/treeIt.h
cpp/treeUtil.cpp
cpp/treeUtil.h
cpp/trivialAccelerator.h
cpp/uniDistribution.cpp
cpp/uniDistribution.h
cpp/uniformDistribution.cpp
cpp/uniformDistribution.h
cpp/ussrvModel.cpp
cpp/ussrvModel.h
cpp/wag.dat.q
cpp/replacementMatrixSource/cpREV45.dat
cpp/replacementMatrixSource/dayhoff.dat
cpp/replacementMatrixSource/jones.dat
cpp/replacementMatrixSource/mitochondriaAscidian.code
cpp/replacementMatrixSource/mitochondriaEchinoderm.code
cpp/replacementMatrixSource/mitochondriaFlatworm.code
cpp/replacementMatrixSource/mitochondriaInvertebrate.code
cpp/replacementMatrixSource/mitochondriaProtozoan.code
cpp/replacementMatrixSource/mitochondriaVertebrate.code
cpp/replacementMatrixSource/mitochondriaYeast.code
cpp/replacementMatrixSource/mtREV24.dat
cpp/replacementMatrixSource/nuclearBlepharisma.code
cpp/replacementMatrixSource/nuclearCiliate.code
cpp/replacementMatrixSource/nuclearEuplotid.code
cpp/replacementMatrixSource/nuclearStandard.code
cpp/replacementMatrixSource/wag.dat
pyrate4site.egg-info/PKG-INFO
pyrate4site.egg-info/SOURCES.txt
pyrate4site.egg-info/dependency_links.txt
pyrate4site.egg-info/not-zip-safe
pyrate4site.egg-info/requires.txt
pyrate4site.egg-info/top_level.txt