Function reference

Models, probability distributions, and functions available in model expressions.

Browse by category below or use the alphabetical index.

Entries describe the current master branch. For help matching your installed version, use bali-phy help NAME.

Models

  • 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
  • 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
  • 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
  • density
  • dNdS — Scale non-synonymous rates by omega
  • Empirical
  • EQU — The equal-exchangeabilities matrix
  • F — The +F frequency model
  • F1x4 — F1x4 codon frequencies
  • F3x4
  • F61
  • F81 — The Felsenstein (1981) rate matrix
  • FE — The +FE frequency model
  • FMutSel
  • FMutSel0
  • Frequencies.uniform
  • 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
  • Inv — Invariable sites modelAliases: I
  • JC69 — The Jukes-Cantor substitution rate matrix
  • JTT
  • K80 — The Kimura (1980) rate matrixAliases: k2p
  • LG
  • LG4M
  • LG4X
  • LG_freq — The LG amino-acid frequencies
  • 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
  • MarkovModulate
  • 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.
  • 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
  • nonEq — Non-equilibrium Markov model
  • nonRev — The General Non-Reversible rate matrixAliases: nonrev
  • PAM
  • ParameterMixture — Mixture model
  • RelaxedRS07 — Redelings & Suchard (2007) model of insertions and deletions.
  • RNA.M16A — Exchangability matrix on doublets constructed from nucleotide exchange ratesAliases: shh01_m16a, RNA.shh01_m16a
  • RNAEdit — RNA editting model
  • RS05 — Redelings & Suchard (2005) model of insertions and deletions
  • RS07 — Redelings & Suchard (2007) model of insertions and deletions.
  • RS07RelaxedRates
  • sample
  • TN93 — The Tamura-Nei (1993) nucleotide rate matrix
  • TN93_sym — The Tamura-Nei (1993) nucleotide exchangability matrix
  • UL2
  • 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

Distributions

Functions