sim_linked | R Documentation |

simulate a sequence assuming conditional substitutions on the node.

```
sim_linked(
phy,
Q = rep(1, 6),
rate = 0.1,
node_mut_rate_double = 1e-09,
l = 1000,
bf = rep(0.25, 4),
rootseq = NULL,
node_time = 0.01
)
```

`phy` |
tree for which to simulate sequences |

`Q` |
substitution matrix along the branches, default = JC |

`rate` |
mutation rate , default = 1 |

`node_mut_rate_double` |
mutation rate on the node, default = 1e-9 |

`l` |
number of base pairs to simulate |

`bf` |
base frequencies, default = c(0.25, 0.25, 0.25, 0.25) |

`rootseq` |
sequence at the root, simulated by default |

`node_time` |
time spent at the node |

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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