sim_normal | R Documentation |

`simSeq`

from the phangorn package.Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function `simSeq`

from the phangorn package.

```
sim_normal(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 |

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

Klaus Schliep klaus.schliep@gmail.com

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