Index of /kundaje/marinovg/oak/various/programs/gainLoss.VR01.261/gainLoss.doubleRep/libs/phylogeny

	Name	Last modified	Size	Description
	Parent Directory		-
	AddLog.cpp	2011-10-22 14:02	593
	AddLog.doubleRep.o	2017-01-18 16:13	3.8K
	AddLog.h	2011-10-22 14:02	1.3K
	C_evalParamUSSRV.cpp	2011-10-22 14:03	2.9K
	C_evalParamUSSRV.doubleRep.o	2017-01-18 16:14	28K
	C_evalParamUSSRV.h	2011-10-22 14:02	4.1K
	ConversionUtils.cpp	2011-10-22 14:02	1.2K
	ConversionUtils.doubleRep.o	2017-01-18 16:13	9.1K
	ConversionUtils.h	2011-10-22 14:02	1.0K
	GLaguer.cpp	2011-10-22 14:02	4.7K
	GLaguer.doubleRep.o	2017-01-18 16:14	14K
	GLaguer.h	2011-10-22 14:02	667
	GamMixtureOptimizer.cpp	2011-10-22 14:02	5.5K
	GamMixtureOptimizer.doubleRep.o	2017-01-18 16:15	24K
	GamMixtureOptimizer.h	2011-10-22 14:02	2.2K
	HIVb.dat.q	2008-09-22 14:40	2.4K
	HIVw.dat.q	2008-09-22 14:40	2.4K
	LG.dat.q	2009-01-20 17:12	2.0K
	Makefile	2017-01-18 14:05	7.5K
	NNiProp.cpp	2011-10-22 14:02	3.8K
	NNiProp.doubleRep.o	2017-01-18 16:13	37K
	NNiProp.h	2011-10-22 14:02	909
	NNiSep.cpp	2011-10-22 14:02	4.6K
	NNiSep.doubleRep.o	2017-01-18 16:13	33K
	NNiSep.h	2011-10-22 14:02	929
	Nni.cpp	2011-10-22 14:02	3.2K
	Nni.doubleRep.o	2017-01-18 16:13	30K
	Nni.h	2011-10-22 14:03	716
	Parameters.cpp	2012-01-05 16:57	8.5K
	Parameters.doubleRep.o	2017-01-18 16:14	35K
	Parameters.h	2011-10-22 14:02	9.3K
	aaJC.cpp	2011-10-22 14:02	97
	aaJC.doubleRep.o	2017-01-18 16:13	2.0K
	aaJC.h	2011-10-22 14:02	1.7K
	adrianCodon.dat.q	2011-10-22 13:51	23K
	allTrees.cpp	2011-10-22 14:02	3.8K
	allTrees.doubleRep.o	2017-01-18 16:13	37K
	allTrees.h	2011-10-22 14:02	1.5K
	allTreesSeparateModel.cpp	2011-10-22 14:02	2.3K
	allTreesSeparateModel.doubleRep.o	2017-01-18 16:13	21K
	allTreesSeparateModel.h	2011-10-22 14:03	2.3K
	alphaTrivialAccelerator.h	2011-10-22 14:02	1.8K
	alphabet.cpp	2011-10-22 14:02	205
	alphabet.doubleRep.o	2017-01-18 16:13	1.5K
	alphabet.h	2011-10-22 14:02	861
	amino.cpp	2011-10-22 14:02	5.0K
	amino.doubleRep.o	2017-01-18 16:13	62K
	amino.h	2011-10-22 14:02	1.3K
	bblEM.cpp	2011-10-22 14:02	7.4K
	bblEM.doubleRep.o	2017-01-18 16:13	122K
	bblEM.h	2011-10-22 14:03	1.6K
	bblEM2USSRV.cpp	2011-10-22 14:02	5.8K
	bblEM2USSRV.doubleRep.o	2017-01-18 16:15	122K
	bblEM2USSRV.h	2011-10-22 14:02	2.5K
	bblEM2codon.cpp	2011-10-22 14:02	5.4K
	bblEM2codon.doubleRep.o	2017-01-18 16:15	128K
	bblEM2codon.h	2011-10-22 14:02	1.6K
	bblEMProportional.h	2011-10-22 14:02	1.6K
	bblEMProportionalEB.cpp	2011-10-22 14:03	10K
	bblEMProportionalEB.doubleRep.o	2017-01-18 16:13	199K
	bblEMProportionalEB.h	2011-10-22 14:02	2.3K
	bblEMProprtional.cpp	2011-10-22 14:02	5.0K
	bblEMProprtional.doubleRep.o	2017-01-18 16:13	159K
	bblEMSeperate.cpp	2011-10-22 14:02	834
	bblEMSeperate.doubleRep.o	2017-01-18 16:13	16K
	bblEMSeperate.h	2011-10-22 14:03	710
	bblEMfixRoot.cpp	2011-10-22 14:02	9.3K
	bblEMfixRoot.doubleRep.o	2017-01-18 16:13	131K
	bblEMfixRoot.h	2011-10-22 14:03	3.2K
	bblLSProportionalEB.cpp	2011-10-22 14:03	2.5K
	bblLSProportionalEB.doubleRep.o	2017-01-18 16:13	18K
	bblLSProportionalEB.h	2011-10-22 14:02	2.0K
	bestAlpha.cpp	2011-12-12 12:15	15K
	bestAlpha.doubleRep.o	2017-01-18 16:13	125K
	bestAlpha.h	2011-12-12 12:15	7.7K
	bestAlphaAndK.cpp	2011-10-22 14:02	10K
	bestAlphaAndK.doubleRep.o	2017-01-18 16:15	47K
	bestAlphaAndK.h	2011-10-22 14:02	2.6K
	bestAlphaAndNu.cpp	2011-10-22 14:03	6.2K
	bestAlphaAndNu.doubleRep.o	2017-01-18 16:14	46K
	bestAlphaAndNu.h	2011-10-22 14:02	6.0K
	bestAlphaManyTrees.cpp	2011-10-22 14:02	7.0K
	bestAlphaManyTrees.doubleRep.o	2017-01-18 16:13	53K
	bestAlphaManyTrees.h	2011-10-22 14:02	3.6K
	bestGtrModelParams.cpp	2011-12-12 12:15	18K
	bestGtrModelParams.doubleRep.o	2017-01-18 16:15	142K
	bestGtrModelParams.h	2011-12-12 12:15	7.2K
	bestHKYparam.cpp	2011-12-12 12:15	12K
	bestHKYparam.doubleRep.o	2017-01-18 16:13	119K
	bestHKYparam.h	2011-12-12 12:15	5.4K
	bestParamUSSRV.cpp	2011-10-22 14:03	16K
	bestParamUSSRV.doubleRep.o	2017-01-18 16:15	62K
	bestParamUSSRV.h	2011-10-22 14:02	3.7K
	bestTamura92param.cpp	2011-12-12 12:15	15K
	bestTamura92param.doubleRep.o	2017-01-18 16:15	132K
	bestTamura92param.h	2011-12-12 12:15	7.9K
	betaDistribution.cpp	2011-10-22 14:02	3.8K
	betaDistribution.doubleRep.o	2017-01-18 16:14	22K
	betaDistribution.h	2011-10-22 14:02	2.2K
	betaDistributionFixedCategories.cpp	2011-10-22 14:02	4.7K
	betaDistributionFixedCategories.doubleRep.o	2017-01-18 16:15	31K
	betaDistributionFixedCategories.h	2011-10-22 14:02	1.6K
	betaDistributionFixedCategoriesWithOmegaUniform.cpp	2011-10-22 14:02	1.8K
	betaDistributionFixedCategoriesWithOmegaUniform.doubleRep.o	2017-01-18 16:15	17K
	betaDistributionFixedCategoriesWithOmegaUniform.h	2011-10-22 14:02	2.7K
	betaOmegaDistribution.cpp	2011-10-22 14:02	1.6K
	betaOmegaDistribution.doubleRep.o	2017-01-18 16:14	16K
	betaOmegaDistribution.h	2011-10-22 14:02	2.5K
	betaUtilities.cpp	2011-10-22 14:02	4.9K
	betaUtilities.doubleRep.o	2017-01-18 16:14	13K
	betaUtilities.h	2011-10-22 14:02	818
	bootstrap.cpp	2011-10-22 14:02	8.1K
	bootstrap.doubleRep.o	2017-01-18 16:13	59K
	bootstrap.h	2011-10-22 14:02	2.7K
	chebyshevAccelerator.cpp	2011-10-22 14:02	6.8K
	chebyshevAccelerator.doubleRep.o	2017-01-18 16:13	46K
	chebyshevAccelerator.h	2011-10-22 14:02	1.6K
	checkcovFanctors.h	2011-10-22 14:02	2.6K
	checkcovFanctorsWithFactors.h	2011-10-22 14:02	1.2K
	clustalFormat.cpp	2011-10-22 14:02	5.2K
	clustalFormat.doubleRep.o	2017-01-18 16:13	25K
	clustalFormat.h	2011-10-22 14:03	1.6K
	cmdline.ggo	2011-10-22 14:02	3.9K
	cmdline2EvolObjs.cpp	2011-10-22 14:02	95
	cmdline2EvolObjs.doubleRep.o	2017-01-18 16:14	2.0K
	cmdline2EvolObjs.h	2011-10-22 14:02	22K
	codon.cpp	2011-10-22 14:02	15K
	codon.doubleRep.o	2017-01-18 16:13	148K
	codon.h	2011-10-22 14:02	4.5K
	codonJC.cpp	2011-10-22 14:02	81
	codonJC.doubleRep.o	2017-01-18 16:13	2.0K
	codonJC.h	2011-10-22 14:02	1.5K
	codonUtils.cpp	2011-10-22 14:02	8.7K
	codonUtils.doubleRep.o	2017-01-18 16:15	50K
	codonUtils.h	2011-10-22 14:02	1.1K
	computeCounts.cpp	2011-10-22 14:02	7.3K
	computeCounts.doubleRep.o	2017-01-18 16:13	30K
	computeCounts.h	2011-10-22 14:02	3.0K
	computeDownAlg.cpp	2011-10-22 14:02	7.6K
	computeDownAlg.doubleRep.o	2017-01-18 16:13	57K
	computeDownAlg.h	2011-10-22 14:02	1.4K
	computeJumps.cpp	2012-12-04 21:41	14K
	computeJumps.doubleRep.o	2017-01-18 16:15	59K
	computeJumps.h	2011-10-22 14:02	4.0K
	computeMarginalAlg.cpp	2011-10-22 14:02	2.9K
	computeMarginalAlg.doubleRep.o	2017-01-18 16:13	19K
	computeMarginalAlg.h	2011-10-22 14:02	890
	computePijComponent.cpp	2011-10-22 14:02	3.0K
	computePijComponent.doubleRep.o	2017-01-18 16:13	67K
	computePijComponent.h	2011-10-22 14:02	1.8K
	computePosteriorExpectationOfSubstitutions.cpp	2011-10-22 14:02	8.7K
	computePosteriorExpectationOfSubstitutions.doubleRep.o	2017-01-18 16:13	69K
	computePosteriorExpectationOfSubstitutions.h	2011-10-22 14:02	2.2K
	computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp	2011-10-22 14:02	4.0K
	computePosteriorExpectationOfSubstitutions_nonReversibleSp.doubleRep.o	2017-01-18 16:13	60K
	computePosteriorExpectationOfSubstitutions_nonReversibleSp.h	2011-10-22 14:02	952
	computeSubstitutionCounts.cpp	2011-10-22 14:02	20K
	computeSubstitutionCounts.doubleRep.o	2017-01-18 16:13	131K
	computeSubstitutionCounts.h	2011-10-22 14:02	3.0K
	computeUpAlg.cpp	2011-10-22 14:02	5.2K
	computeUpAlg.doubleRep.o	2017-01-18 16:13	81K
	computeUpAlg.h	2011-10-22 14:02	1.9K
	computeUpAlgFactors.cpp	2011-10-22 14:02	6.7K
	computeUpAlgFactors.doubleRep.o	2017-01-18 16:13	69K
	countTableComponent.cpp	2011-10-22 14:02	1.0K
	countTableComponent.doubleRep.o	2017-01-18 16:13	15K
	countTableComponent.h	2011-10-22 14:03	4.4K
	cpREV45.dat.q	2011-10-22 13:52	1.2K
	datMatrixHolder.cpp	2011-10-22 14:02	753
	datMatrixHolder.doubleRep.o	2017-01-18 16:13	57K
	datMatrixHolder.h	2011-10-22 14:02	935
	dayhoff.dat.q	2011-10-22 13:52	4.0K
	definitions.h	2012-05-29 18:02	2.6K
	distanceBasedSeqs2Tree.cpp	2011-10-22 14:02	23K
	distanceBasedSeqs2Tree.doubleRep.o	2017-01-18 16:14	113K
	distanceBasedSeqs2Tree.h	2011-10-22 14:03	12K
	distanceMethod.h	2011-10-22 14:02	664
	distanceTable.cpp	2011-10-22 14:03	708
	distanceTable.doubleRep.o	2017-01-18 16:13	18K
	distanceTable.h	2011-10-22 14:03	398
	distances2Tree.h	2011-10-22 14:03	439
	distribution.cpp	2011-10-22 14:02	412
	distribution.doubleRep.o	2017-01-18 16:13	4.8K
	distribution.h	2011-10-22 14:02	1.1K
	distributionPlusCategory.cpp	2011-10-22 14:02	2.6K
	distributionPlusCategory.doubleRep.o	2017-01-18 16:15	24K
	distributionPlusCategory.h	2011-10-22 14:02	1.6K
	distributionPlusInvariant.cpp	2011-10-22 14:02	1.8K
	distributionPlusInvariant.doubleRep.o	2017-01-18 16:15	22K
	distributionPlusInvariant.h	2011-10-22 14:02	1.7K
	doubleRep.cpp	2011-10-22 14:02	1.4K
	doubleRep.doubleRep.o	2017-01-18 16:14	936
	doubleRep.h	2011-10-22 14:02	8.5K
	errorMsg.cpp	2017-01-18 14:10	1.2K
	errorMsg.doubleRep.o	2017-01-18 16:13	7.0K
	errorMsg.h	2011-10-22 14:02	777
	evaluateCharacterFreq.cpp	2012-03-21 23:37	4.2K
	evaluateCharacterFreq.doubleRep.o	2017-01-18 16:13	27K
	evaluateCharacterFreq.h	2011-10-22 14:03	1.1K
	extremeValDistribution.cpp	2012-05-29 18:02	1.7K
	extremeValDistribution.doubleRep.o	2017-01-18 16:15	5.4K
	extremeValDistribution.h	2012-05-29 18:02	1.1K
	fastStartTree.cpp	2011-10-22 14:02	4.0K
	fastStartTree.doubleRep.o	2017-01-18 16:14	49K
	fastStartTree.h	2011-10-22 14:02	514
	fastaFormat.cpp	2012-03-11 11:58	2.0K
	fastaFormat.doubleRep.o	2017-01-18 16:14	11K
	fastaFormat.h	2011-10-22 14:02	1.3K
	findRateOfGene.cpp	2011-10-22 14:02	2.3K
	findRateOfGene.doubleRep.o	2017-01-18 16:14	11K
	findRateOfGene.h	2011-10-22 14:03	593
	fromCountTableComponentToDistance.cpp	2011-10-22 14:02	919
	fromCountTableComponentToDistance.doubleRep.o	2017-01-18 16:14	11K
	fromCountTableComponentToDistance.h	2011-10-22 14:03	1.1K
	fromCountTableComponentToDistance2Codon.cpp	2011-10-22 14:02	771
	fromCountTableComponentToDistance2Codon.doubleRep.o	2017-01-18 16:15	8.1K
	fromCountTableComponentToDistance2Codon.h	2011-10-22 14:02	1.0K
	fromCountTableComponentToDistance2USSRV.cpp	2011-10-22 14:02	780
	fromCountTableComponentToDistance2USSRV.doubleRep.o	2017-01-18 16:15	9.5K
	fromCountTableComponentToDistance2USSRV.h	2011-10-22 14:02	1.2K
	fromCountTableComponentToDistanceProp.cpp	2011-10-22 14:02	629
	fromCountTableComponentToDistanceProp.doubleRep.o	2017-01-18 16:14	2.9K
	fromCountTableComponentToDistanceProp.h	2011-10-22 14:02	1.0K
	fromCountTableComponentToDistancePropEB.cpp	2011-10-22 14:02	1.0K
	fromCountTableComponentToDistancePropEB.doubleRep.o	2017-01-18 16:14	5.8K
	fromCountTableComponentToDistancePropEB.h	2011-10-22 14:03	1.2K
	fromCountTableComponentToDistancefixRoot.cpp	2011-10-22 14:02	1.0K
	fromCountTableComponentToDistancefixRoot.doubleRep.o	2017-01-18 16:14	11K
	fromCountTableComponentToDistancefixRoot.h	2011-10-22 14:02	1.3K
	fromInstructionFile.cpp	2011-10-22 14:02	18K
	fromInstructionFile.h	2011-10-22 14:02	2.1K
	fromQtoPt.cpp	2011-10-22 14:03	9.3K
	fromQtoPt.doubleRep.o	2017-01-18 16:14	32K
	fromQtoPt.h	2011-10-22 14:03	2.0K
	gainLossAlphabet.cpp	2011-10-22 14:03	2.2K
	gainLossAlphabet.doubleRep.o	2017-01-18 16:15	34K
	gainLossAlphabet.h	2011-10-22 14:02	918
	gammaDistribution.cpp	2011-10-22 14:02	1.3K
	gammaDistribution.doubleRep.o	2017-01-18 16:14	16K
	gammaDistribution.h	2011-10-22 14:02	1.5K
	gammaDistributionFixedCategories.cpp	2011-10-22 14:03	1.2K
	gammaDistributionFixedCategories.doubleRep.o	2017-01-18 16:15	18K
	gammaDistributionFixedCategories.h	2011-10-22 14:02	1.8K
	gammaDistributionLaguerre.cpp	2011-10-22 14:02	1.4K
	gammaDistributionLaguerre.doubleRep.o	2017-01-18 16:14	16K
	gammaDistributionLaguerre.h	2011-10-22 14:02	1.7K
	gammaDistributionPlusInvariant.cpp	2011-10-22 14:02	99
	gammaDistributionPlusInvariant.doubleRep.o	2017-01-18 16:15	2.1K
	gammaDistributionPlusInvariant.h	2011-10-22 14:02	1.5K
	gammaUtilities.cpp	2011-10-22 14:02	4.4K
	gammaUtilities.doubleRep.o	2017-01-18 16:14	13K
	gammaUtilities.h	2012-09-19 03:32	2.3K
	generalGammaDistribution.cpp	2011-10-22 14:02	3.1K
	generalGammaDistribution.doubleRep.o	2017-01-18 16:14	24K
	generalGammaDistribution.h	2011-10-22 14:02	2.3K
	generalGammaDistributionFixedCategories.cpp	2011-10-22 14:02	9.8K
	generalGammaDistributionFixedCategories.doubleRep.o	2017-01-18 16:14	37K
	generalGammaDistributionFixedCategories.h	2011-10-22 14:02	1.7K
	generalGammaDistributionLaguerre.cpp	2011-10-22 14:02	3.1K
	generalGammaDistributionLaguerre.doubleRep.o	2017-01-18 16:14	21K
	generalGammaDistributionLaguerre.h	2011-10-22 14:03	2.1K
	generalGammaDistributionPlusInvariant.cpp	2011-10-22 14:02	113
	generalGammaDistributionPlusInvariant.doubleRep.o	2017-01-18 16:15	2.1K
	generalGammaDistributionPlusInvariant.h	2011-10-22 14:02	2.5K
	geneticCodeHolder.cpp	2011-10-22 14:02	1.5K
	geneticCodeHolder.doubleRep.o	2017-01-18 16:14	11K
	geneticCodeHolder.h	2011-10-22 14:02	1.1K
	getRandomWeights.cpp	2011-10-22 14:02	1.4K
	getRandomWeights.doubleRep.o	2017-01-18 16:14	6.0K
	getRandomWeights.h	2011-10-22 14:02	1.0K
	getopt.h	2011-10-22 14:03	6.3K
	givenRatesMLDistance.cpp	2011-10-22 14:03	4.8K
	givenRatesMLDistance.doubleRep.o	2017-01-18 16:14	27K
	givenRatesMLDistance.h	2011-10-22 14:03	1.8K
	goldmanYangModel.cpp	2011-10-22 14:02	3.6K
	goldmanYangModel.doubleRep.o	2017-01-18 16:14	35K
	goldmanYangModel.h	2011-10-22 14:02	1.8K
	granthamChemicalDistances.cpp	2011-10-22 14:02	8.2K
	granthamChemicalDistances.doubleRep.o	2017-01-18 16:14	19K
	granthamChemicalDistances.h	2011-10-22 14:03	852
	gtrModel.cpp	2011-10-22 14:03	5.2K
	gtrModel.doubleRep.o	2017-01-18 16:15	41K
	gtrModel.h	2011-10-22 14:02	1.8K
	hky.cpp	2011-10-22 14:02	12K
	hky.doubleRep.o	2017-01-18 16:14	24K
	hky.h	2011-10-22 14:02	1.2K
	indel.cpp	2011-10-22 14:02	1.4K
	indel.doubleRep.o	2017-01-18 16:14	21K
	indel.h	2011-10-22 14:02	900
	indelModel.cpp	2011-10-22 14:02	304
	indelModel.doubleRep.o	2017-01-18 16:14	2.6K
	indelModel.h	2011-10-22 14:02	1.3K
	integerAlphabet.cpp	2011-10-22 14:02	1.7K
	integerAlphabet.doubleRep.o	2017-01-18 16:15	16K
	integerAlphabet.h	2011-10-22 14:02	876
	jcDistance.h	2011-10-22 14:02	4.3K
	jones.dat.q	2007-11-28 09:59	12K
	khTest.cpp	2011-10-22 14:02	1.6K
	khTest.doubleRep.o	2017-01-18 16:14	7.0K
	khTest.h	2011-10-22 14:02	182
	libEvolTreeDoubleRep.a	2017-01-18 16:15	6.5M
	likeDist.cpp	2011-10-22 14:03	12K
	likeDist.doubleRep.o	2017-01-18 16:14	64K
	likeDist.h	2011-10-22 14:02	8.1K
	likeDist2Codon.cpp	2011-10-22 14:02	788
	likeDist2Codon.doubleRep.o	2017-01-18 16:15	13K
	likeDist2Codon.h	2011-10-22 14:03	3.8K
	likeDist2USSRV.cpp	2011-10-22 14:02	2.2K
	likeDist2USSRV.doubleRep.o	2017-01-18 16:15	16K
	likeDist2USSRV.h	2011-10-22 14:02	5.1K
	likeDistProp.cpp	2011-10-22 14:02	617
	likeDistProp.doubleRep.o	2017-01-18 16:14	19K
	likeDistProp.h	2011-10-22 14:02	2.6K
	likeDistPropEB.cpp	2011-10-22 14:02	774
	likeDistPropEB.doubleRep.o	2017-01-18 16:14	23K
	likeDistPropEB.h	2011-10-22 14:02	5.0K
	likeDistfixRoot.cpp	2011-10-22 14:02	13K
	likeDistfixRoot.doubleRep.o	2017-01-18 16:14	40K
	likeDistfixRoot.h	2011-10-22 14:02	8.9K
	likelihoodComputation.cpp	2011-10-22 14:02	23K
	likelihoodComputation.doubleRep.o	2017-01-18 16:14	95K
	likelihoodComputation.h	2011-10-22 14:02	7.8K
	likelihoodComputation2Codon.cpp	2011-10-22 14:02	2.6K
	likelihoodComputation2Codon.doubleRep.o	2017-01-18 16:15	50K
	likelihoodComputation2Codon.h	2011-10-22 14:02	1.1K
	likelihoodComputation2USSRV.cpp	2011-10-22 14:02	2.6K
	likelihoodComputation2USSRV.doubleRep.o	2017-01-18 16:15	28K
	likelihoodComputation2USSRV.h	2011-10-22 14:02	1.1K
	likelihoodComputationFactors.cpp	2011-10-22 14:02	1.0K
	likelihoodComputationFactors.doubleRep.o	2017-01-18 16:14	5.1K
	likelihoodComputationFactors.h	2011-10-22 14:02	594
	likelihoodComputationGL.cpp	2011-10-22 14:02	14K
	likelihoodComputationGL.doubleRep.o	2017-01-18 16:15	71K
	likelihoodComputationGL.h	2011-10-22 14:02	3.8K
	logFile.cpp	2011-10-22 14:02	1.2K
	logFile.doubleRep.o	2017-01-18 16:14	9.6K
	logFile.h	2011-10-22 14:02	1.2K
	logRep.cpp	2011-10-22 14:02	431
	logRep.doubleRep.o	2017-01-18 16:14	2.5K
	logRep.h	2011-10-22 14:03	4.2K
	make.dep	2017-01-18 14:00	52K
	maseFormat.cpp	2011-10-22 14:02	2.5K
	maseFormat.doubleRep.o	2017-01-18 16:14	16K
	maseFormat.h	2011-10-22 14:02	1.4K
	matrixUtils.cpp	2011-10-22 14:02	8.0K
	matrixUtils.doubleRep.o	2017-01-18 16:14	72K
	matrixUtils.h	2017-01-18 14:27	4.5K
	mixtureDistribution.cpp	2011-10-22 14:03	9.9K
	mixtureDistribution.doubleRep.o	2017-01-18 16:15	32K
	mixtureDistribution.h	2011-10-22 14:02	4.0K
	molphyFormat.cpp	2011-10-22 14:02	2.5K
	molphyFormat.doubleRep.o	2017-01-18 16:14	9.4K
	molphyFormat.h	2011-10-22 14:02	1.3K
	mtREV24.dat.q	2007-11-28 09:59	2.4K
	mulAlphabet.cpp	2011-10-22 14:02	4.3K
	mulAlphabet.doubleRep.o	2017-01-18 16:14	25K
	mulAlphabet.h	2011-10-22 14:03	1.6K
	multipleStochasticProcess.cpp	2011-10-22 14:02	869
	multipleStochasticProcess.doubleRep.o	2017-01-18 16:15	10K
	multipleStochasticProcess.h	2011-10-22 14:02	604
	nexusFormat.cpp	2011-10-22 14:02	5.2K
	nexusFormat.doubleRep.o	2017-01-18 16:14	27K
	nexusFormat.h	2011-10-22 14:02	1.8K
	nj.cpp	2011-10-23 15:51	13K
	nj.doubleRep.o	2017-01-18 16:14	49K
	nj.h	2011-10-22 14:02	3.1K
	njConstrain.cpp	2011-10-22 14:03	4.7K
	njConstrain.doubleRep.o	2017-01-18 16:14	39K
	njConstrain.h	2011-10-22 14:02	703
	normalDist.cpp	2011-10-22 14:02	1.6K
	normalDist.doubleRep.o	2017-01-18 16:15	6.3K
	normalDist.h	2011-10-22 14:02	1.0K
	nucJC.cpp	2011-10-22 14:02	76
	nucJC.doubleRep.o	2017-01-18 16:14	2.0K
	nucJC.h	2011-10-22 14:03	1.7K
	nucleotide.cpp	2011-10-22 14:02	4.6K
	nucleotide.doubleRep.o	2017-01-18 16:14	48K
	nucleotide.h	2011-10-22 14:02	3.5K
	numRec.cpp	2011-10-22 14:02	12K
	numRec.doubleRep.o	2017-01-18 16:14	43K
	numRec.h	2011-10-22 14:02	12K
	oneTwoMoreModel.cpp	2011-10-22 16:34	7.7K
	oneTwoMoreModel.doubleRep.o	2017-01-18 16:15	53K
	oneTwoMoreModel.h	2011-10-22 16:34	4.5K
	optGammaMixtureEM.cpp	2011-10-22 14:02	10K
	optGammaMixtureEM.doubleRep.o	2017-01-18 16:15	60K
	optGammaMixtureEM.h	2011-10-22 14:02	3.6K
	optGammaMixtureLS.cpp	2011-10-22 14:02	9.4K
	optGammaMixtureLS.doubleRep.o	2017-01-18 16:15	61K
	optGammaMixtureLS.h	2011-10-22 14:02	8.7K
	pDistance.h	2011-10-22 14:02	1.1K
	pairwiseGammaDistance.cpp	2011-10-22 14:02	5.0K
	pairwiseGammaDistance.doubleRep.o	2017-01-18 16:14	33K
	pairwiseGammaDistance.h	2011-10-22 14:02	2.0K
	phylipFormat.cpp	2011-10-22 14:02	4.3K
	phylipFormat.doubleRep.o	2017-01-18 16:14	15K
	phylipFormat.h	2011-10-22 14:02	1.7K
	phylipSequentialFormat.cpp	2011-10-22 14:02	4.3K
	phylipSequentialFormat.doubleRep.o	2017-01-18 16:15	12K
	phylipSequentialFormat.h	2011-10-22 14:02	1.2K
	pijAccelerator.cpp	2011-10-22 14:02	231
	pijAccelerator.doubleRep.o	2017-01-18 16:14	2.4K
	pijAccelerator.h	2011-10-22 14:02	744
	posteriorDistance.cpp	2011-10-22 14:02	15K
	posteriorDistance.doubleRep.o	2017-01-18 16:14	75K
	posteriorDistance.h	2011-10-22 14:02	2.2K
	readDatMatrix.cpp	2011-10-22 14:02	7.9K
	readDatMatrix.doubleRep.o	2017-01-18 16:14	66K
	readDatMatrix.h	2011-10-22 14:02	2.6K
	readTree.cpp	2011-10-22 14:02	5.1K
	readTree.doubleRep.o	2017-01-18 16:14	14K
	readTree.h	2011-10-22 14:02	1.1K
	recognizeFormat.cpp	2011-10-22 14:02	2.6K
	recognizeFormat.doubleRep.o	2017-01-18 16:14	15K
	recognizeFormat.h	2011-10-22 14:02	516
	replacementMatrixSource/	2017-01-18 13:56	-
	replacementModel.cpp	2011-10-22 14:03	239
	replacementModel.doubleRep.o	2017-01-18 16:14	2.4K
	replacementModel.h	2011-10-22 14:02	912
	replacementModelSSRV.cpp	2011-10-22 14:02	4.8K
	replacementModelSSRV.doubleRep.o	2017-01-18 16:14	34K
	replacementModelSSRV.h	2011-10-22 14:03	2.6K
	samplingSequences.cpp	2011-10-22 14:02	5.5K
	samplingSequences.doubleRep.o	2017-01-18 16:15	40K
	samplingSequences.h	2011-10-22 14:03	961
	searchStatus.cpp	2011-10-22 14:02	217
	searchStatus.doubleRep.o	2017-01-18 16:14	4.4K
	searchStatus.h	2011-10-22 14:03	652
	seqContainerTreeMap.cpp	2011-10-22 14:02	5.2K
	seqContainerTreeMap.doubleRep.o	2017-01-18 16:14	39K
	seqContainerTreeMap.h	2011-10-22 14:02	1.1K
	seqeuncesFilter.cpp	2011-10-22 14:02	6.5K
	seqeuncesFilter.doubleRep.o	2017-01-18 16:15	24K
	seqeuncesFilter.h	2011-10-22 14:02	1.3K
	sequence.cpp	2011-10-22 14:02	5.2K
	sequence.doubleRep.o	2017-01-18 16:14	21K
	sequence.h	2011-10-22 14:02	3.9K
	sequenceContainer.cpp	2012-03-21 23:37	14K
	sequenceContainer.doubleRep.o	2017-01-18 16:14	56K
	sequenceContainer.h	2012-01-10 19:29	6.2K
	simulateCodonsJumps.cpp	2011-10-22 14:02	11K
	simulateCodonsJumps.doubleRep.o	2017-01-18 16:15	64K
	simulateCodonsJumps.h	2011-10-22 14:02	2.6K
	simulateJumps.cpp	2011-10-22 14:02	7.1K
	simulateJumps.doubleRep.o	2017-01-18 16:15	66K
	simulateJumps.h	2011-10-22 14:02	2.3K
	simulateJumpsAbstract.cpp	2011-10-22 14:02	1.3K
	simulateJumpsAbstract.doubleRep.o	2017-01-18 16:15	9.2K
	simulateJumpsAbstract.h	2011-10-22 14:02	3.5K
	simulateRateShiftJumps.cpp	2011-10-22 14:02	14K
	simulateRateShiftJumps.doubleRep.o	2017-01-18 16:15	71K
	simulateRateShiftJumps.h	2011-10-22 14:02	2.8K
	simulateTree.cpp	2011-10-22 14:02	7.5K
	simulateTree.doubleRep.o	2017-01-18 16:14	56K
	simulateTree.h	2011-10-22 14:02	1.8K
	siteSpecificRate.cpp	2012-11-04 22:11	18K
	siteSpecificRate.doubleRep.o	2017-01-18 16:14	81K
	siteSpecificRate.h	2012-11-04 22:11	5.7K
	siteSpecificRateGL.cpp	2011-10-22 14:02	11K
	siteSpecificRateGL.h	2011-10-22 14:02	4.9K
	someUtil.cpp	2017-01-18 14:21	29K
	someUtil.doubleRep.o	2017-01-18 16:14	99K
	someUtil.h	2012-05-30 15:36	7.5K
	split.cpp	2011-10-22 14:02	2.4K
	split.doubleRep.o	2017-01-18 16:14	11K
	split.h	2011-10-22 14:02	1.7K
	splitMap.cpp	2011-10-22 14:02	1.2K
	splitMap.doubleRep.o	2017-01-18 16:14	34K
	splitMap.h	2011-10-22 14:02	1.1K
	splitTreeUtil.cpp	2011-10-22 14:02	3.9K
	splitTreeUtil.doubleRep.o	2017-01-18 16:14	15K
	splitTreeUtil.h	2011-10-22 14:02	817
	ssrvDistanceSeqs2Tree.cpp	2011-10-22 14:02	5.7K
	ssrvDistanceSeqs2Tree.doubleRep.o	2017-01-18 16:15	19K
	ssrvDistanceSeqs2Tree.h	2011-10-22 14:02	3.5K
	stochasticProcess.cpp	2011-10-22 14:03	1.6K
	stochasticProcess.doubleRep.o	2017-01-18 16:14	10K
	stochasticProcess.h	2011-10-22 14:03	2.1K
	stochasticProcessSSRV.cpp	2011-10-22 14:02	667
	stochasticProcessSSRV.doubleRep.o	2017-01-18 16:14	11K
	stochasticProcessSSRV.h	2011-10-22 14:02	2.1K
	suffStatComponent.cpp	2011-10-22 14:02	101
	suffStatComponent.doubleRep.o	2017-01-18 16:14	2.0K
	suffStatComponent.h	2011-10-22 14:02	8.7K
	suffStatGammaMixture.cpp	2011-10-22 14:02	7.3K
	suffStatGammaMixture.doubleRep.o	2017-01-18 16:15	36K
	suffStatGammaMixture.h	2011-10-22 14:03	2.0K
	talRandom.cpp	2011-10-22 14:03	2.2K
	talRandom.doubleRep.o	2017-01-18 16:14	5.1K
	talRandom.h	2011-10-22 14:02	2.9K
	tamura92.cpp	2011-10-22 14:03	5.4K
	tamura92.doubleRep.o	2017-01-18 16:15	16K
	tamura92.h	2011-10-22 14:02	1.0K
	threeStateAlphabet.cpp	2011-10-22 14:02	1.5K
	threeStateAlphabet.doubleRep.o	2017-01-18 16:15	26K
	threeStateAlphabet.h	2011-10-22 14:02	894
	threeStateModel.cpp	2011-10-22 14:02	7.5K
	threeStateModel.doubleRep.o	2017-01-18 16:15	79K
	threeStateModel.h	2011-10-22 14:02	4.5K
	tree.cpp	2012-05-13 19:25	40K
	tree.doubleRep.o	2017-01-18 16:14	129K
	tree.h	2011-10-22 14:02	9.2K
	treeInference.cpp	2011-10-22 14:02	523
	treeInference.h	2011-10-22 14:02	565
	treeIt.cpp	2011-10-22 14:02	103
	treeIt.doubleRep.o	2017-01-18 16:14	2.0K
	treeIt.h	2011-10-22 14:03	3.4K
	treeUtil.cpp	2012-03-21 23:37	13K
	treeUtil.doubleRep.o	2017-01-18 16:14	103K
	treeUtil.h	2012-03-21 23:37	1.5K
	trivialAccelerator.h	2011-10-22 14:02	1.3K
	unObservableData.cpp	2011-10-22 14:02	3.5K
	unObservableData.doubleRep.o	2017-01-18 16:15	61K
	unObservableData.h	2011-10-22 14:02	1.5K
	uniDistribution.cpp	2011-10-22 14:02	352
	uniDistribution.doubleRep.o	2017-01-18 16:14	9.7K
	uniDistribution.h	2011-10-22 14:02	1.1K
	uniformDistribution.cpp	2011-10-22 14:02	1.9K
	uniformDistribution.doubleRep.o	2017-01-18 16:14	17K
	uniformDistribution.h	2011-10-22 14:02	2.0K
	ussrvModel.cpp	2011-10-22 14:03	4.1K
	ussrvModel.doubleRep.o	2017-01-18 16:15	13K
	ussrvModel.h	2011-10-22 14:03	1.5K
	wYangModel.cpp	2011-10-22 14:02	2.4K
	wYangModel.doubleRep.o	2017-01-18 16:15	54K
	wYangModel.h	2011-10-22 14:02	1.7K
	wag.dat.q	2007-11-28 09:59	3.3K