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