Bio.Phylo.Consensus module

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.

Bio.Phylo.Consensus.strict_consensus(trees)

Search strict consensus tree from multiple trees.

Parameters:
treesiterable

iterable of trees to produce consensus tree.

Bio.Phylo.Consensus.majority_consensus(trees, cutoff=0)

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:
treesiterable

iterable of trees to produce consensus tree.

Bio.Phylo.Consensus.adam_consensus(trees)

Search Adam Consensus tree from multiple trees.

Parameters:
treeslist

list of trees to produce consensus tree.

Bio.Phylo.Consensus.get_support(target_tree, trees, len_trees=None)

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

Parameters:
target_treeTree

tree to calculate branch support for.

treesiterable

iterable of trees used to calculate branch support.

len_treesint

optional count of replicates in trees. len_trees must be provided when len(trees) is not a valid operation.

Bio.Phylo.Consensus.bootstrap(msa, times)

Generate bootstrap replicates from a multiple sequence alignment (OBSOLETE).

Parameters:
msaMultipleSeqAlignment

multiple sequence alignment to generate replicates.

timesint

number of bootstrap times.

Bio.Phylo.Consensus.bootstrap_trees(alignment, times, tree_constructor)

Generate bootstrap replicate trees from a multiple sequence alignment.

Parameters:
alignmentAlignment or MultipleSeqAlignment object

multiple sequence alignment to generate replicates.

timesint

number of bootstrap times.

tree_constructorTreeConstructor

tree constructor to be used to build trees.

Bio.Phylo.Consensus.bootstrap_consensus(alignment, times, tree_constructor, consensus)

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

Parameters:
alignmentAlignment or MultipleSeqAlignment object

Multiple sequence alignment to generate replicates.

timesint

Number of bootstrap times.

tree_constructorTreeConstructor

Tree constructor to be used to build trees.

consensusfunction

Consensus method in this module: strict_consensus, majority_consensus, adam_consensus.