For a more detailed explanation, see `vignette("sub-models")`

.

sub_TN93(pi_tcag, alpha_1, alpha_2, beta) sub_JC69(lambda) sub_K80(alpha, beta) sub_F81(pi_tcag) sub_HKY85(pi_tcag, alpha, beta) sub_F84(pi_tcag, beta, kappa) sub_GTR(pi_tcag, abcdef) sub_UNREST(Q)

pi_tcag | Vector of length 4 indicating the equilibrium distributions of T, C, A, and G respectively. Values must be >= 0, and they are forced to sum to 1. |
---|---|

alpha_1 | Substitution rate for T <-> C transition. |

alpha_2 | Substitution rate for A <-> G transition. |

beta | Substitution rate for transversions. |

lambda | Substitution rate for all possible substitutions. |

alpha | Substitution rate for transitions. |

kappa | The transition/transversion rate ratio. |

abcdef | A vector of length 6 that contains the off-diagonal elements
for the substitution rate matrix.
See |

Q | Matrix of substitution rates for "T", "C", "A", and "G", respectively.
Item |

A `sub_model_info`

object, which is just a wrapper around a list with
fields `Q`

and `pi_tcag`

. The former has the rate matrix, and the latter
has the equilibrium nucleotide densities for "T", "C", "A", and "G", respectively.
Access the rate matrix for a `sub_model_info`

object named `x`

via `x$Q`

and
densities via `x$pi_tcag`

.

`sub_TN93`

: TN93 model.`sub_JC69`

: JC69 model.`sub_K80`

: K80 model.`sub_F81`

: F81 model.`sub_HKY85`

: HKY85 model.`sub_F84`

: F84 model.`sub_GTR`

: GTR model.`sub_UNREST`

: UNREST model.

# Same substitution rate for all types: Q_JC69 <- sub_JC69(lambda = 0.1) # Transitions 2x more likely than transversions: Q_K80 <- sub_K80(alpha = 0.2, beta = 0.1) # Same as above, but incorporating equilibrium frequencies sub_HKY85(pi_tcag = c(0.1, 0.2, 0.3, 0.4), alpha = 0.2, beta = 0.1)#> < Substitution information > #> # Equilibrium densities: #> 0.1000 0.2000 0.3000 0.4000 #> # Substitution rate matrix: #> T C A G #> T 0.00 0.04 0.03 0.04 #> C 0.02 0.00 0.03 0.04 #> A 0.01 0.02 0.00 0.08 #> G 0.01 0.02 0.06 0.00 #> (View rate matrix in the "Q" field) #> (View equil. densities in the "pi_tcag" field)