Description Usage Arguments Value Examples

Computes the maximum likelihood parameters for a given tree topology.

1 | ```
MLparameters(x, tree, freq = NULL)
``` |

`x` |
a binary matrix whose rows are the (preferably unique) genetic profiles. |

`tree` |
the tree in matrix format. |

`freq` |
a vector whose length equals the number of rows of x, giving the frequency of each profile in the data. |

`p` |
a vector of the maximum likelihood edge parameters (model probabilities). |

`totloglik` |
the log-likelihood at the ML parameters. |

1 2 |

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