Index

_

__init__() (phydmslib.models.ExpCM method) (phydmslib.models.ExpCM_empirical_phi method) (phydmslib.models.ExpCM_empirical_phi_divpressure method) (phydmslib.models.ExpCM_fitprefs method) (phydmslib.models.GammaDistributedBetaModel method) (phydmslib.models.GammaDistributedModel method) (phydmslib.models.GammaDistributedOmegaModel method) (phydmslib.models.YNGKP_M0 method) (phydmslib.treelikelihood.TreeLikelihood method)

A

ALLOWEDPARAMS (phydmslib.models.ExpCM attribute) (phydmslib.models.ExpCM_empirical_phi attribute) (phydmslib.models.ExpCM_empirical_phi_divpressure attribute) (phydmslib.models.ExpCM_fitprefs attribute) (phydmslib.models.YNGKP_M0 attribute)

ArgDefaultsRawDescriptFormatter (class in phydmslib.parsearguments) ArgumentParserNoArgHelp (class in phydmslib.parsearguments)

B

basemodel() (phydmslib.models.DistributionModel property) (phydmslib.models.GammaDistributedModel property) BenjaminiHochbergCorrection() (in module phydmslib.utils) branchScale() (phydmslib.models.ExpCM property) (phydmslib.models.GammaDistributedModel property) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property)

broadcastGetCols() (in module phydmslib.numutils) broadcastMatrixMultiply() (in module phydmslib.numutils) broadcastMatrixVectorMultiply() (in module phydmslib.numutils)

C

catweights() (phydmslib.models.DistributionModel property) (phydmslib.models.GammaDistributedModel property)

ChargeColorMapping() (in module phydmslib.weblogo)

D

d_distributionparams() (phydmslib.models.DistributionModel property) (phydmslib.models.GammaDistributedModel property) diffPrefsPrior() (in module phydmslib.parsearguments) DiscreteGamma() (in module phydmslib.models) distributedparam() (phydmslib.models.DistributionModel property) (phydmslib.models.GammaDistributedModel property) DistributionModel (class in phydmslib.models) distributionparams() (phydmslib.models.DistributionModel property) (phydmslib.models.GammaDistributedModel property) dloglik() (phydmslib.treelikelihood.TreeLikelihood property) dloglik_dt() (phydmslib.treelikelihood.TreeLikelihood property) dloglikarray() (phydmslib.treelikelihood.TreeLikelihood property) dlogprior() (phydmslib.models.ExpCM method) (phydmslib.models.ExpCM_fitprefs method) (phydmslib.models.GammaDistributedModel method) (phydmslib.models.Model method) (phydmslib.models.YNGKP_M0 method)

dM() (phydmslib.models.DistributionModel method) (phydmslib.models.ExpCM method) (phydmslib.models.GammaDistributedModel method) (phydmslib.models.Model method) (phydmslib.models.YNGKP_M0 method) dparamscurrent() (phydmslib.treelikelihood.TreeLikelihood property) dstationarystate() (phydmslib.models.DistributionModel method) (phydmslib.models.ExpCM method) (phydmslib.models.GammaDistributedModel method) (phydmslib.models.Model method) (phydmslib.models.YNGKP_M0 method) dtcurrent() (phydmslib.treelikelihood.TreeLikelihood property)

E

error() (phydmslib.parsearguments.ArgumentParserNoArgHelp method) ExistingFile() (in module phydmslib.parsearguments) ExistingFileOrNone() (in module phydmslib.parsearguments) ExpCM (class in phydmslib.models)

ExpCM_empirical_phi (class in phydmslib.models) ExpCM_empirical_phi_divpressure (class in phydmslib.models) ExpCM_fitprefs (class in phydmslib.models) ExpCM_fitprefs2 (class in phydmslib.models)

F

FloatBetweenZeroAndOne() (in module phydmslib.parsearguments) FloatGreaterThanEqualToZero() (in module phydmslib.parsearguments) FloatGreaterThanOne() (in module phydmslib.parsearguments) FloatGreaterThanZero() (in module phydmslib.parsearguments)

freeparams() (phydmslib.models.ExpCM property) (phydmslib.models.GammaDistributedModel property) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property) FunctionalGroupColorMapping() (in module phydmslib.weblogo)

G

GammaDistributedBetaModel (class in phydmslib.models)

GammaDistributedModel (class in phydmslib.models) GammaDistributedOmegaModel (class in phydmslib.models)

I

IntGreaterThanOne() (in module phydmslib.parsearguments)

IntGreaterThanZero() (in module phydmslib.parsearguments)

K

KyteDoolittleColorMapping() (in module phydmslib.weblogo)

L

LogoOverlay() (in module phydmslib.weblogo) LogoPlot() (in module phydmslib.weblogo) logprior() (phydmslib.models.ExpCM property) (phydmslib.models.ExpCM_fitprefs property) (phydmslib.models.GammaDistributedModel property) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property)

M

M() (phydmslib.models.DistributionModel method) (phydmslib.models.ExpCM method) (phydmslib.models.GammaDistributedModel method) (phydmslib.models.Model method) (phydmslib.models.YNGKP_M0 method) maximizeLikelihood() (phydmslib.treelikelihood.TreeLikelihood method) Model (class in phydmslib.models) modelComparisonDataFrame() (in module phydmslib.utils) ModelOption() (in module phydmslib.parsearguments) module phydmslib phydmslib.constants phydmslib.file_io phydmslib.models phydmslib.numutils phydmslib.parsearguments phydmslib.simulate phydmslib.treelikelihood phydmslib.utils phydmslib.weblogo

mu() (phydmslib.models.ExpCM property) (phydmslib.models.GammaDistributedModel property) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property) MWColorMapping() (in module phydmslib.weblogo)

N

ncats() (phydmslib.models.DistributionModel property) (phydmslib.models.GammaDistributedModel property) NonNegativeInt() (in module phydmslib.parsearguments)

nsites() (phydmslib.models.ExpCM property) (phydmslib.models.GammaDistributedModel property) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property)

P

PARAMLIMITS() (phydmslib.models.ExpCM property) (phydmslib.models.GammaDistributedModel property) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property) paramsarray() (phydmslib.treelikelihood.TreeLikelihood property) paramsarraybounds() (phydmslib.treelikelihood.TreeLikelihood property) paramsReport() (phydmslib.models.ExpCM property) (phydmslib.models.GammaDistributedModel property) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property) PARAMTYPES (phydmslib.models.ExpCM attribute) (phydmslib.models.ExpCM_empirical_phi attribute) (phydmslib.models.ExpCM_empirical_phi_divpressure attribute) (phydmslib.models.GammaDistributedModel attribute) (phydmslib.models.YNGKP_M0 attribute) PhyDMSComprehensiveParser() (in module phydmslib.parsearguments) phydmslib module phydmslib.constants module

phydmslib.file_io module phydmslib.models module phydmslib.numutils module phydmslib.parsearguments module phydmslib.simulate module phydmslib.treelikelihood module phydmslib.utils module phydmslib.weblogo module PhyDMSLogoPlotParser() (in module phydmslib.parsearguments) PhyDMSParser() (in module phydmslib.parsearguments) PhyDMSPrepAlignmentParser() (in module phydmslib.parsearguments) PhyDMSTestdivpressureParser() (in module phydmslib.parsearguments) pyvolvePartitions() (in module phydmslib.simulate)

R

ReadCodonAlignment() (in module phydmslib.file_io) readDivPressure() (in module phydmslib.file_io)

readPrefs() (in module phydmslib.file_io) readPrefs_dms_tools_format() (in module phydmslib.file_io)

S

simulateAlignment() (in module phydmslib.simulate) SingleColorMapping() (in module phydmslib.weblogo) spielman_wr() (phydmslib.models.ExpCM method) stationarystate() (phydmslib.models.DistributionModel method) (phydmslib.models.ExpCM property) (phydmslib.models.GammaDistributedModel method) (phydmslib.models.Model property) (phydmslib.models.YNGKP_M0 property)

T

t() (phydmslib.treelikelihood.TreeLikelihood property)

tree() (phydmslib.treelikelihood.TreeLikelihood property) TreeLikelihood (class in phydmslib.treelikelihood)

U

updateParams() (phydmslib.models.ExpCM method) (phydmslib.models.GammaDistributedModel method) (phydmslib.models.Model method) (phydmslib.models.YNGKP_M0 method) (phydmslib.treelikelihood.TreeLikelihood method)

V

Versions() (in module phydmslib.file_io)

Y

YNGKP_M0 (class in phydmslib.models)