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 object.

Parameters

msaMultipleSeqAlignment

multiple sequence alignment to generate replicates.

timesint

number of bootstrap times.

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

Generate bootstrap replicate trees from a multiple sequence alignment.

Parameters

msaMultipleSeqAlignment

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(msa, times, tree_constructor, consensus)

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

Parameters

msaMultipleSeqAlignment

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.