Alphabetical index
- != — The inequality operator
- % — The modulo operator
- && — The and operator
- *
- + — The addition operator
- -
- .*.
- /
- < — The less-than operator
- <= — The less-than-or-equals operator
- == — The equality operator
- > — The greater-than operator
- >= — The greater-than-or-equals operator
- AA — The amino-acid alphabet
-
ASRV.Free — Free rates modelAliases:
R -
ASRV.Gamma — The Gamma rate
heterogeneity modelAliases:
G - ASRV.Gamma_mean — The conditional-mean Gamma rate heterogeneity model
- ASRV.Gamma_median — The median-discretized Gamma rate heterogeneity model
- ASRV.Gamma_quadrature — The quadrature-discretized Gamma rate heterogeneity model
- ASRV.LogNormal
- Bernoulli — The Bernoulli distribution
- Beta — The Beta distribution
- Binomial — Binomial distribution
- branch_length
- branches
- branches_list
- BranchModel — Multiple-omega branch model
- BranchModel_test — Bayesian test of branch-category assignment hypotheses
- BranchSite — The branch-site test for positive selection from Zhang et al. (2005)
- BranchSiteMixture
- BUSTED
- BUSTED_S
- C10 — Mixture model
- C10_fixed — Mixture model
- C20 — Mixture model
- C20_fixed — Mixture model
- C30 — Mixture model
- C30_fixed — Mixture model
- C40 — Mixture model
- C40_fixed — Mixture model
- C50 — Mixture model
- C50_fixed — Mixture model
- C60 — Mixture model
- C60_fixed — Mixture model
- Cauchy — The Cauchy-Lorentz distribution
- cdf — The cumulative distribution function
- codons — The codons alphabet
- Cons — cons: append to the front of a list
- convertDiscrete — Convert a discrete distribution to a distribution
- cos — The cosine function
- Covarion.Galtier01 — The Galtier (2001) Covarion Model
- Covarion.GTR — The General Reversity Covarion Model
- Covarion.Huelsenbeck02 — The Huelsenbeck Covarion Model
- Covarion.Huelsenbeck02_test — The Huelsenbeck Covarion Model
- Covarion.Huelsenbeck02Two — The Huelsenbeck Covarion Model
- Covarion.MultiFreq
- Covarion.TuffleySteel98 — The Tuffley-Steel Covarion Model
- Covarion.Wang07 — The WSSR (2007) Covarion Model
- delta — The Dirac delta distribution
- density
- Dirichlet — The Dirichlet distribution
- DirichletMixture — Dirichlet mixture model
- DirichletOn
-
DirichletOnDirichlet
— Free rates modelAliases:
DP - DirichletProcess — The Dirichlet process distribution
- DirichletProcessMap — The integer-map Dirichlet process distribution
- DirichletProcessMixture — The Dirichlet process mixture distribution
- DirichletProcessOn — The keyed Dirichlet process distribution
- discrete
- discreteFromMap
- DNA — The DNA alphabet
-
dNdS — Scale non-synonymous rates by
omega - doublets — The doublets alphabet
- Empirical
- EQU — The equal-exchangeabilities matrix
- exp — The exponential function
- Exponential — The Exponential distribution
- F — The +F frequency model
- F1x4 — F1x4 codon frequencies
- F3x4
- F61
- F81 — The Felsenstein (1981) rate matrix
- FE — The +FE frequency model
- FixedTopologyTree — The uniform_topology distribution on trees
- FMutSel
- FMutSel0
- Frequencies.uniform
- Gamma — The gamma distribution
- Geometric — The Geometric distribution
- getAminoAcids
- getNucleotides
- getQ
- GTR — The General Time-Reversible rate matrix
- GTR_sym — The GTR exchangability matrix
- gwF
-
GY94 — The Goldman & Yang (1994) model
of dN/dSAliases:
m0 - GY94_ext — An extended version of the Goldman & Yang (1994) model of dN/dS
- HKY85 — The Hasegawa-Kishino-Yano (1985) nucleotide rate matrix
- HKY85_sym — The Hasegawa-Kishino-Yano (1985) nucleotide exchangabilty matrix
- identity
- IID — The Independent and Identically Distributed (i.i.d.) distribution
- IIDMap — The Independent and Identically Distributed (i.i.d.) distribution
- IIDOn — The Independent and Identically Distributed (i.i.d.) distribution
- intToDouble — Function to convert an integer to a double-precision number:
-
Inv — Invariable sites modelAliases:
I - JC69 — The Jukes-Cantor substitution rate matrix
- JTT
-
K80 — The Kimura (1980) rate matrixAliases:
k2p - Laplace — The Laplace distribution
- length
- letter_pairs
- letters
- LG
- LG4M
- LG4X
- LG_freq — The LG amino-acid frequencies
- log — The natural logarithm
- LogCauchy — The log-cauchy distribution
- LogGamma
- LogLaplace
- LogNormal — The log-normal distribution
- lookup
- M1a
- M2a
-
M2a_testAliases:
M2a_Test - M3 — The M3 model
-
M3_testAliases:
M3_Test - M7
- M8
- M8a
-
M8a_test — Bayesian version of the M8a
test for positive selectionAliases:
M8a_Test - map
- mapFromList
- MarkovModulate
- max — The maximum of two numbers
- MG94 — The Muse & Gaut (1994) model of dN/dS.
- MG94_ext — An extended version of the Muse & Gaut (1994) model of codon substitution.
- MG94K — The Muse & Gaut (1994) model of codon substitution.
- min — The minimum of two numbers
-
mixture — Mixture modelAliases:
Mixture - MNM — Rate matrix on triplets/codons that includes multi-nucleotide mutations
- MultiFreq
- MultiRate
- MultiRS07 — Redelings & Suchard (2007) model of insertions and deletions.
- MutSel — Mutation-selection model with fitness values for codons
-
MutSelAA — Mutation-selection model
with fitness values for amino-acidsAliases:
mut_sel0 - n_components
- negate
- Nil — The empty list
- nodes
- nonEq — Non-equilibrium Markov model
-
nonRev — The General Non-Reversible rate
matrixAliases:
nonrev - nonreversible — The exponential function
- Normal — The normal distribution
- num_branches
- number_pairs
- numberBranchCategories
- numberBranchHypotheses
- numberHypothesisBranchCategories
- ordered_letter_pairs
- ordered_letters
- PAM
- ParameterMixture — Mixture model
- pdf — The probability density function
- Poisson — The Poisson distribution
- pow
- quantile — The quantile function
- RelaxedRS07 — Redelings & Suchard (2007) model of insertions and deletions.
- replicate — The replicate function
- RNA — The RNA alphabet
-
RNA.M16A — Exchangability matrix on
doublets constructed from nucleotide exchange ratesAliases:
shh01_m16a,RNA.shh01_m16a - RNAEdit — RNA editting model
- rnaEditsOf — The RNA-edits alphabet
- RS05 — Redelings & Suchard (2005) model of insertions and deletions
- RS07 — Redelings & Suchard (2007) model of insertions and deletions.
- RS07RelaxedRates
- sample
- scaleBy — The scaleBy function
- scaleTo — The scaleTo function
- selectBranchHypothesis
- setFromList
- ShiftedExponential — The Exponential distribution
- ShiftedGamma — The gamma distribution
- sin — The sine function
- sort
- sqrt — The square-root function
- standard_code — The standard genetic code
- sum
- SymmetricDirichlet — The Dirichlet distribution
- SymmetricDirichletOn
- take
- tan — The tangent function
- TN93 — The Tamura-Nei (1993) nucleotide rate matrix
- TN93_sym — The Tamura-Nei (1993) nucleotide exchangability matrix
- triplets — The triplets alphabet
- UL2
- Uniform — The Uniform distribution
- uniform_discretize — Uniformly discretize a continuous distribution
- UniformInt — Uniform distribution on integers
- UniformRootedTree — The uniform_topology distribution on trees
- UniformTree — The uniform_topology distribution on trees
-
unit_mixtureAliases:
UnitMixture - WAG
- WAG_freq — The WAG amino-acid frequencies
- x2 — Rate matrix on doublets constructed from nucleotide rates
- x2_sym — Exchangability matrix on doublets constructed from nucleotide exchange rates
- x2x2 — Rate matrix constructed from rate matrices on each doublet position
- x3 — Rate matrix on triplets/codons constructed from nucleotide rates
- x3_sym — Exchangability matrix on triplets/codon constructed from nucleotide exchange rates
- x3x3 — Rate matrix constructed from rate matrices on each triplet position
- Yule — The uniform_topology distribution on trees
- zip
- zipWith
- |+|
- || — The or operator