Simulate DNA Alignments Using Node Substitutions

calc_expected_hidden_nodes | Calculate the number of expected hidden nodes in a... |

calc_fraction | Calculate the expected fraction of substitutions at the... |

calc_required_node_time | Calculate the required node time to obtain a desired fraction... |

calc_sum_stats | calculate summary statistics of a phylogenetic tree, compared... |

count_hidden | Function to calculate the number of hidden speciation events,... |

create_balanced_tree | create a balanced tree out of branching times |

create_equal_alignment | function create an alignment with identical information... |

create_equal_alignment_explicit | function create an alignment with identical information... |

create_unbalanced_tree | create an unbalanced tree out of branching times |

estimate_marginal_models | estimate the marginal likelihood of the relaxed and strict... |

get_p_matrix | calculate p matrix |

infer_phylogeny | infer the time calibrated phylogeny associated with the... |

nodeSub-package | Package providing functions to simulate sequences under... |

reduce_tree | Function to remove speciation events occuring after an... |

sim_linked | simulate a sequence assuming conditional substitutions on the... |

sim_normal | Simulate sequences for a given evolutionary tree, using a... |

sim_normal_explicit | simulate a sequence assuming substitutions are only... |

sim_unlinked | Simulate a sequence assuming node substitutions are not... |

sim_unlinked_explicit | Simulate a sequence assuming node substitutions are not... |

slow_matrix | this function calculates the p matrix within R this is slower... |

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