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Name Date Size #Lines LOC

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2RatesAnalyses/H14-Oct-2021-1,8961,657

Distances/H14-Oct-2021-1,2931,114

GUI/H14-Oct-2021-21

Miscellaneous/phylohandbook/H14-Oct-2021-1,9611,605

ProteinAnalyses/H14-Oct-2021-1,167854

Samplers/H14-Oct-2021-927730

SelectionAnalyses/H14-Oct-2021-13,90510,468

TemplateModels/H14-Oct-2021-23,67921,534

Utility/H14-Oct-2021-6,5535,457

libv3/H14-Oct-2021-19,19616,125

AAModelComparison.bfH A D14-Oct-20215.3 KiB243188

AddABias.ibfH A D14-Oct-20219 KiB284235

AnalyzeCodonData.bfH A D14-Oct-20211.2 KiB5436

AnalyzeDiNucData.bfH A D14-Oct-2021661 2915

AnalyzeNucDataFreq.bfH A D14-Oct-2021869 4327

AnalyzeNucProtData.bfH A D14-Oct-2021868 2918

BGM.bfH A D14-Oct-202119.9 KiB415313

BivariateCodonRateAnalysis.bfH A D14-Oct-20213 KiB12190

BranchSiteREL.bfH A D14-Oct-202138.2 KiB1,094843

BranchSiteRELMultiModel.bfH A D14-Oct-202120.1 KiB576443

CleanGaps.bfH A D14-Oct-20213.2 KiB11596

CleanStopCodons.bfH A D14-Oct-20215.5 KiB198162

ClusterAnalysis.bfH A D14-Oct-202110.4 KiB536454

ClusterByDistanceRange.bfH A D14-Oct-202113.5 KiB605496

CodonBivariateRateProcessor.bfH A D14-Oct-202110.7 KiB423316

CodonModelCompare.bfH A D14-Oct-202125.5 KiB1,047947

CodonToProtein.bfH A D14-Oct-20214.9 KiB182150

ConvertDataFile.bfH A D14-Oct-20212.2 KiB5947

DirectionalREL.bfH A D14-Oct-202117.6 KiB593480

DistanceMatrix.bfH A D14-Oct-20217.8 KiB313268

F_ST.bfH A D14-Oct-202117.4 KiB645527

FitnessAAModels.bfH A D14-Oct-20217.9 KiB341297

GARD.bfH A D14-Oct-202148.8 KiB1,106899

GA_CHC.ibfH A D14-Oct-202111.2 KiB459417

GA_CHC_Binary.ibfH A D14-Oct-202114 KiB600538

Gateaux.bfH A D14-Oct-20218.1 KiB333276

GateauxMR.bfH A D14-Oct-20217.6 KiB329271

KHTest.bfH A D14-Oct-20216.5 KiB267220

LEISR.bfH A D14-Oct-202123.5 KiB494355

LHT.bfH A D14-Oct-20216.4 KiB215192

LRTRecombTest.bfH A D14-Oct-20217.6 KiB310267

LZ_Complexity.bfH A D14-Oct-20211.9 KiB6755

LocalMolClock.bfH A D14-Oct-20215 KiB201159

MGvsGY.bfH A D14-Oct-202115.6 KiB641562

MergeSequences.bfH A D14-Oct-2021958 3830

MergeSites.bfH A D14-Oct-2021966 3830

ModelTest.bfH A D14-Oct-202119.1 KiB726602

MolClockAllRoots.bfH A D14-Oct-20215.6 KiB231180

MolecularClock.bfH A D14-Oct-20213.2 KiB148107

NeighborJoining.bfH A D14-Oct-20214.1 KiB190150

NielsenYang.bfH A D14-Oct-202131.8 KiB1,2341,104

NucModelCompare.bfH A D14-Oct-202124 KiB1,088968

PARRIS.bfH A D14-Oct-202141.7 KiB1,4281,279

PairwiseRelativeRate.bfH A D14-Oct-20217.3 KiB280223

PairwiseRelativeRatio.bfH A D14-Oct-20219.6 KiB341283

PartitionDataFile.bfH A D14-Oct-20211.8 KiB4635

ReduceDataSetMatrix.bfH A D14-Oct-20218.9 KiB406358

RelativeRate.bfH A D14-Oct-20213.4 KiB161123

RelativeRatio.bfH A D14-Oct-20215.4 KiB259200

SGASimProcessor.bfH A D14-Oct-202112.9 KiB550463

SGEmulator.bfH A D14-Oct-202122.9 KiB922789

SGEmulator_MF.bfH A D14-Oct-202119.1 KiB744643

SGIvL.bfH A D14-Oct-202118.4 KiB759648

SM-2019.bfH A D14-Oct-202112.5 KiB318229

SandNSAmbigs.bfH A D14-Oct-20219.3 KiB458372

SelectionLRT.bfH A D14-Oct-202110.6 KiB368276

SeqAlignShared.ibfH A D14-Oct-202183 KiB784686

SeqAlignmentCodon.bfH A D14-Oct-2021169 84

SeqAlignmentCodonShared.ibfH A D14-Oct-20217.7 KiB213173

SeqAlignmentNucShared.ibfH A D14-Oct-20217 KiB291225

SequentialAddition.bfH A D14-Oct-20215.4 KiB166123

SequentialAddition.ibfH A D14-Oct-202114.9 KiB617553

SimilarityPlot.bfH A D14-Oct-20214.5 KiB168136

SimmondsAI.bfH A D14-Oct-20217.6 KiB318263

SingleBreakpointRecomb.bfH A D14-Oct-202128.7 KiB1,184993

SlidingWindowAnalysis.bfH A D14-Oct-20216.3 KiB280240

TestBranchDNDS.bfH A D14-Oct-202112 KiB447369

TestClade.bfH A D14-Oct-202123.2 KiB1,069946

TestCladeMeans.bfH A D14-Oct-202110.1 KiB421343

TopologySearch.bfH A D14-Oct-202110.5 KiB499436

TopologySearchConstrained.bfH A D14-Oct-20218.9 KiB411358

TreeCorrelationCoefficients.bfH A D14-Oct-20217.8 KiB338278

TreeTools.ibfH A D14-Oct-202120.2 KiB820696

UpperBound.bfH A D14-Oct-20211.6 KiB6451

WANC.bfH A D14-Oct-20219.1 KiB380318

YangNielsenBranchSite2005.bfH A D14-Oct-202114.3 KiB496409

_BMS_Aux.ibfH A D14-Oct-20214.4 KiB175158

_CMS_Aux.ibfH A D14-Oct-20218.6 KiB345309

_MFReader_.ibfH A D14-Oct-20216.8 KiB223190

_tipDater.ibfH A D14-Oct-20211.8 KiB8476

bayesgraph.ibfH A D14-Oct-202120 KiB846691

binomial.ibfH A D14-Oct-20211.6 KiB9077

branchSwappingFunctions.bfH A D14-Oct-20218.7 KiB412384

categoryEcho.bfH A D14-Oct-20214.3 KiB170161

chooseDistanceFormula.defH A D14-Oct-20213.9 KiB9689

dNdSBivariateRateAnalysis.bfH A D14-Oct-202121.5 KiB828685

dNdSDistributionComparison.bfH A D14-Oct-202128.6 KiB1,029829

dNdSRateAnalysis.bfH A D14-Oct-202126.2 KiB981848

dNdSResultProcessor.bfH A D14-Oct-202132.1 KiB1,2431,079

dSdNTreeTools.ibfH A D14-Oct-20212.6 KiB10587

distanceMethodNPBootstrap.bfH A D14-Oct-20219.5 KiB444396

distanceRMethodNPBootstrap.bfH A D14-Oct-20217.7 KiB374335

doNNISwap.bfH A D14-Oct-20213 KiB151144

doSPRSwap.bfH A D14-Oct-20212.8 KiB134130

files.lstH A D14-Oct-202111.7 KiB11392

globalChecker.ibfH A D14-Oct-2021511 2725

heuristicMethodNPBootstrap.bfH A D14-Oct-20215.8 KiB274255

last.dateH A D14-Oct-202115 21

molclockBootstrap.bfH A D14-Oct-20215.9 KiB246220

pairwiseDistanceEstimator.ibfH A D14-Oct-202110.3 KiB371324

pairwiseDistanceEstimatorCounter.ibfH A D14-Oct-2021180 1110

partitionSequences.ibfH A D14-Oct-20211.6 KiB6753

posteriors.ibfH A D14-Oct-2021696 2721

qndhelper1.ibfH A D14-Oct-202135.2 KiB1,2311,059

qndhelper1_mf.ibfH A D14-Oct-20217.4 KiB311266

qndhelper2.ibfH A D14-Oct-202113.2 KiB432370

qndhelper2_mf.ibfH A D14-Oct-202113.8 KiB449389

qndhelper3.ibfH A D14-Oct-20214.3 KiB150145

qndhelper4.ibfH A D14-Oct-20214.3 KiB175152

queryTree.bfH A D14-Oct-20212.8 KiB143130

readIndexFile.bfH A D14-Oct-2021448 2218

relative_nucleotide_rates.bfH A D14-Oct-202112.3 KiB265174

relrateBootstrap.bfH A D14-Oct-20219.9 KiB376345

relratioBootstrap.bfH A D14-Oct-20214.4 KiB132120

selectModelParameters.bfH A D14-Oct-2021449 2014

simpleBootstrap.bfH A D14-Oct-20219.7 KiB390349