Module:Bio::Tree::TreeFunctionsI

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Bio::Tree::TreeFunctionsI
PDoc Bio::Tree::TreeFunctionsI
CPAN Bio::Tree::TreeFunctionsI
metaCPAN Bio::Tree::TreeFunctionsI


Contents

A tree is made up of Bio::Tree::Node objects.

Key Functions

This module implements several functions on a tree.

find_node

Find a node by its name or other attribute.

remove_Node

Remove a node from the tree, takes care of re-connecting the orphaned nodes when this is an internal node. The method is used as part of the reroot.

get_lineage_nodes

For a given node in a tree, get a list of all its ancestor nodes, from root->immediate ancestor of given node.

splice

Remove one or more nodes from a tree without making the tree fall apart.

get_lca

Finds the least common ancestor (LCA) for a set of nodes.

merge_lineage

Add a lineage of nodes to an existing tree.

contract_linear_paths

Splices out all nodes in the tree that have an ancestor and only one descendent.

distance

Calculates the branch length distance between a pair of nodes.

is_monophyletic

This method peforms a test of monophy for a set of nodes given an outgroup. It will first find the (LCA) (returned by get_lca) and then test if the outgroup is a child of the LCA.

is_paraphyletic

Returns
  • -1 if the group is not monophyletic
  • 0 if the group is not paraphyletic
  • 1 if the group is paraphyletic

reroot

Reposition the root of a tree, this involves adding and removing an internal node which serves as the root. The new rooted node will be the midpoint distance between the two internal nodes where the root is placed.

findnode_by_id

Finds a node by its ID (not the autogenerated unique_id)

move_id_to_bootstrap

Assumes the internal node IDs represent the bootstrap values, move them to the bootstrap slot so they can be retrieved with bootstrap() function

Wishlist

  1. collapse function to post-process a bootstrapped tree and collapse nodes below a minimum.
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