View source: R/sim_normal_explicit.R

sim_normal_explicit | R Documentation |

simulate a sequence assuming substitutions are only accumulated along the branches, using the explicit simulation method (e.g. reverse substitutions are modeled explicitly)

```
sim_normal_explicit(x, l = 1000, Q = NULL, bf = NULL, rootseq = NULL, rate = 1)
```

`x` |
a phylogenetic tree |

`l` |
length of the sequence to simulate. |

`Q` |
the rate matrix. |

`bf` |
base frequencies. |

`rootseq` |
a vector of length l containing the root sequence, other root sequence is randomly generated. |

`rate` |
mutation rate or scaler for the edge length, a numerical value greater than zero. |

list with four items

alignment Phydat object with the resulting alignment

rootseq the rootsequence used

total_branch_substitutions total number of substitutions accumulated on the branches

total_node_substitutions total number of substitutions accumulated at the nodes

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