A Collection of Tools for Phylogenetic Tree Manipulation

ancestral_edges | For a node in a tree, get a vector of the edges between the... |

are_bipartitions_compatible | Check if two bipartitions drawn from trees with the same tips... |

bipartition_for_edge | Get a bipartition, described as a vector of tip numbers, from... |

bipartition_for_edge_by_label | Get a bipartition, described as a vector of tip labels, from... |

calc_diffs | For each internal node, calculate the difference in state... |

compatible_edges | Identify the edges in one phylo object that are compatible... |

connecting_edges | For two nodes in a tree, get a vector of the edges that... |

cut_tree | Cuts a single tree on the branch subtending a specified node |

decompose_tree | Decomposes a single tree into a series of subtrees designated... |

descendants | Get all the descendants of a given node in a tree. |

difference_from_calibrated | Assesses how much phy deviates from an ultrametric tree |

distance_from_tip | For each node in the tree (including internal nodes and tips)... |

extend_terminal_branches | Extends each terminal branch by specified length |

flip_bipartition | Given a tree and a bipartition, described as a vector of tip... |

generate_constaint_tree | Generates a tree with a single resolved bipartition between... |

get_bipartitions | Get a list of all the bipartitions in a tree. |

get_corresponding_nodes | Given two trees phy1 and phy2 with the same topology and tip... |

hutan | hutan: A collection of tools for phylogenetic tree... |

is_compatible_with_set | Check if bipartition bi is compatible with the bipartitions... |

is_monophyletic | Test if a set of tips, specified as a vector of tip labels,... |

picx | Estimate the extended phylogenetic independent contrast.... |

safe.drop.tip | Drops specified tips from a phylogeny. Like ape's drop.tip(),... |

sim_diffs | For each internal node, simulate the difference between state... |

siphonophore_constraint | Siphonophores constraint phylogeny. |

siphonophore_ml | Siphonophores phylogeny. |

slide_root_edges | Repartitions lengths along edges that descend from root node... |

tip_descendants | Get all the tips that are descendants of a given node in a... |

tips | Get tips and labels of a phylo object. |

zero_constrained | Generates the "zero-constrained" tree described by Susko 2014... |

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