Index

alphabet
1 (Function)	ELynx.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.MarkovProcess.MixtureModel
alphaToPamlVec	ELynx.MarkovProcess.AminoAcid
appendName	ELynx.MarkovProcess.SubstitutionModel
appendNameComponents	ELynx.MarkovProcess.MixtureModel
c10StatDists	ELynx.MarkovProcess.CXXModelsData
c10Weights	ELynx.MarkovProcess.CXXModelsData
c20StatDists	ELynx.MarkovProcess.CXXModelsData
c20Weights	ELynx.MarkovProcess.CXXModelsData
c30StatDists	ELynx.MarkovProcess.CXXModelsData
c30Weights	ELynx.MarkovProcess.CXXModelsData
c40StatDists	ELynx.MarkovProcess.CXXModelsData
c40Weights	ELynx.MarkovProcess.CXXModelsData
c50StatDists	ELynx.MarkovProcess.CXXModelsData
c50Weights	ELynx.MarkovProcess.CXXModelsData
c60StatDists	ELynx.MarkovProcess.CXXModelsData
c60Weights	ELynx.MarkovProcess.CXXModelsData
Component	ELynx.MarkovProcess.MixtureModel
components	ELynx.MarkovProcess.MixtureModel
concatenate	ELynx.MarkovProcess.MixtureModel
cxx	ELynx.MarkovProcess.CXXModels
EDMComponent	ELynx.Import.MarkovProcess.EDMModelPhylobayes
ExchangeabilityMatrix	ELynx.MarkovProcess.RateMatrix
exchangeabilityMatrix	ELynx.MarkovProcess.SubstitutionModel
exchFromListLower	ELynx.MarkovProcess.RateMatrix
exchFromListUpper	ELynx.MarkovProcess.RateMatrix
expand	ELynx.MarkovProcess.GammaRateHeterogeneity
f81	ELynx.MarkovProcess.Nucleotide
fromExchangeabilityMatrix	ELynx.MarkovProcess.RateMatrix
fromSubstitutionModels	ELynx.MarkovProcess.MixtureModel
getAlphabet	ELynx.MarkovProcess.PhyloModel
getStationaryDistribution	ELynx.MarkovProcess.RateMatrix
getSubstitutionModels	ELynx.MarkovProcess.MixtureModel
getWeights	ELynx.MarkovProcess.MixtureModel
gtr20	ELynx.MarkovProcess.AminoAcid
gtr4	ELynx.MarkovProcess.Nucleotide
hky	ELynx.MarkovProcess.Nucleotide
isValid	ELynx.MarkovProcess.RateMatrix
jc	ELynx.MarkovProcess.Nucleotide
jump	ELynx.Simulate.MarkovProcess
lg	ELynx.MarkovProcess.AminoAcid
lgCustom	ELynx.MarkovProcess.AminoAcid
MixtureModel
1 (Type/Class)	ELynx.MarkovProcess.MixtureModel
2 (Data Constructor)	ELynx.MarkovProcess.PhyloModel
Name	ELynx.MarkovProcess.SubstitutionModel
name
1 (Function)	ELynx.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.MarkovProcess.MixtureModel
normalize
1 (Function)	ELynx.MarkovProcess.RateMatrix
2 (Function)	ELynx.MarkovProcess.SubstitutionModel
3 (Function)	ELynx.MarkovProcess.MixtureModel
normalizeSD	ELynx.MarkovProcess.RateMatrix
normalizeWith	ELynx.MarkovProcess.RateMatrix
pamlToAlphaVec	ELynx.MarkovProcess.AminoAcid
Params	ELynx.MarkovProcess.SubstitutionModel
params	ELynx.MarkovProcess.SubstitutionModel
phylobayes	ELynx.Import.MarkovProcess.EDMModelPhylobayes
PhyloModel	ELynx.MarkovProcess.PhyloModel
poisson	ELynx.MarkovProcess.AminoAcid
poissonCustom	ELynx.MarkovProcess.AminoAcid
ProbMatrix	ELynx.Simulate.MarkovProcess
probMatrix	ELynx.Simulate.MarkovProcess
RateMatrix	ELynx.MarkovProcess.RateMatrix
rateMatrix	ELynx.MarkovProcess.SubstitutionModel
scale
1 (Function)	ELynx.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.MarkovProcess.MixtureModel
setDiagonal	ELynx.MarkovProcess.RateMatrix
simulate	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlatten	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlattenMixtureModel	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlattenMixtureModelPar	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlattenPar	ELynx.Simulate.MarkovProcessAlongTree
simulateMixtureModel	ELynx.Simulate.MarkovProcessAlongTree
siteprofiles	ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
State	ELynx.Simulate.MarkovProcess
StationaryDistribution	ELynx.MarkovProcess.RateMatrix
stationaryDistribution	ELynx.MarkovProcess.SubstitutionModel
SubstitutionModel
1 (Type/Class)	ELynx.MarkovProcess.SubstitutionModel
2 (Data Constructor)	ELynx.MarkovProcess.PhyloModel
substitutionModel	ELynx.MarkovProcess.SubstitutionModel
substModel	ELynx.MarkovProcess.MixtureModel
summarizeGammaRateHeterogeneity	ELynx.MarkovProcess.GammaRateHeterogeneity
toExchangeabilityMatrix	ELynx.MarkovProcess.RateMatrix
totalRate
1 (Function)	ELynx.MarkovProcess.RateMatrix
2 (Function)	ELynx.MarkovProcess.SubstitutionModel
totalRateWith	ELynx.MarkovProcess.RateMatrix
wag	ELynx.MarkovProcess.AminoAcid
wagCustom	ELynx.MarkovProcess.AminoAcid
Weight	ELynx.MarkovProcess.MixtureModel
weight	ELynx.MarkovProcess.MixtureModel