biopython

v1.71.0

biopython v1.71.0 Bio.Phylo.Consensus

Classes and methods for finding consensus trees.

This module contains a _BitString class to assist the consensus tree searching and some common consensus algorithms such as strict, majority rule and adam consensus.

Link to this section Summary

Functions

_bitstring_topology()

Generates a branch length dict for a tree, keyed by BitStrings

_clade_to_bitstr()

Create a BitString representing a clade, given ordered tree taxon names

_count_clades()

Count distinct clades (different sets of terminal names) in the trees

_equal_topology()

Are two trees are equal in terms of topology and branch lengths

_part()

Recursive function of adam consensus algorithm

_sub_clade()

Extract a compatible subclade that only contains the given terminal names

_tree_to_bitstrs()

Create a dict of a tree’s clades to corresponding BitStrings

adam_consensus()

Search Adam Consensus tree from multiple trees

bootstrap()

Generate bootstrap replicates from a multiple sequence alignment object

bootstrap_consensus()

Consensus tree of a series of bootstrap trees for a multiple sequence alignment

bootstrap_trees()

Generate bootstrap replicate trees from a multiple sequence alignment

get_support()

Calculate branch support for a target tree given bootstrap replicate trees

majority_consensus()

Search majority rule consensus tree from multiple trees

strict_consensus()

Search strict consensus tree from multiple trees

Link to this section Functions

Link to this function _bitstring_topology()

Generates a branch length dict for a tree, keyed by BitStrings.

Create a dict of all clades’ BitStrings to the corresponding branch lengths (rounded to 5 decimal places).

Link to this function _clade_to_bitstr()

Create a BitString representing a clade, given ordered tree taxon names.

Link to this function _count_clades()

Count distinct clades (different sets of terminal names) in the trees.

Return a tuple first a dict of bitstring (representing clade) and a tuple of its count of occurrences and sum of branch length for that clade, second the number of trees processed.

:Parameters:

trees : iterable
    An iterable that returns the trees to count
Link to this function _equal_topology()

Are two trees are equal in terms of topology and branch lengths.

(Branch lengths checked to 5 decimal places.)

Link to this function _part()

Recursive function of adam consensus algorithm

Link to this function _sub_clade()

Extract a compatible subclade that only contains the given terminal names

Link to this function _tree_to_bitstrs()

Create a dict of a tree’s clades to corresponding BitStrings.

Link to this function adam_consensus()

Search Adam Consensus tree from multiple trees

:Parameters:

trees : list
    list of trees to produce consensus tree.
Link to this function bootstrap()

Generate bootstrap replicates from a multiple sequence alignment object

:Parameters:

msa : MultipleSeqAlignment
    multiple sequence alignment to generate replicates.
times : int
    number of bootstrap times.
Link to this function bootstrap_consensus()

Consensus tree of a series of bootstrap trees for a multiple sequence alignment

:Parameters:

msa : MultipleSeqAlignment
    Multiple sequence alignment to generate replicates.
times : int
    Number of bootstrap times.
tree_constructor : TreeConstructor
    Tree constructor to be used to build trees.
consensus : function
    Consensus method in this module: `strict_consensus`,
    `majority_consensus`, `adam_consensus`.
Link to this function bootstrap_trees()

Generate bootstrap replicate trees from a multiple sequence alignment.

:Parameters:

msa : MultipleSeqAlignment
    multiple sequence alignment to generate replicates.
times : int
    number of bootstrap times.
tree_constructor : TreeConstructor
    tree constructor to be used to build trees.
Link to this function get_support()

Calculate branch support for a target tree given bootstrap replicate trees.

:Parameters:

target_tree : Tree
    tree to calculate branch support for.
trees : iterable
    iterable of trees used to calculate branch support.
len_trees : int
    optional count of replicates in trees. len_trees must be provided
    when len(trees) is not a valid operation.
Link to this function majority_consensus()

Search majority rule consensus tree from multiple trees.

This is a extend majority rule method, which means the you can set any cutoff between 0 ~ 1 instead of 0.5. The default value of cutoff is 0 to create a relaxed binary consensus tree in any condition (as long as one of the provided trees is a binary tree). The branch length of each consensus clade in the result consensus tree is the average length of all counts for that clade.

:Parameters:

trees : iterable
    iterable of trees to produce consensus tree.
Link to this function strict_consensus()

Search strict consensus tree from multiple trees.

:Parameters:

trees : iterable
    iterable of trees to produce consensus tree.