consensus_tree

piqtree.consensus_tree(trees, *, min_support=0.5, support_aggregate='mean')

Build a consensus tree, defaults to majority-rule consensus tree.

The min_support parameter represents the proportion of trees a clade must appear in to be in the resulting consensus tree.

If min_support is 1.0, computes the strict consensus tree. If min_support is 0.0, computes the extended majority-rule consensus tree.

By default the input trees' own support values are transferred onto matching consensus clades.

PARAMETER	DESCRIPTION
trees	The trees to form a consensus tree from. TYPE: Iterable[PhyloNode]
min_support	The minimum support for a clade to appear in the consensus tree, by default 0.5. TYPE: float DEFAULT: 0.5
support_aggregate	How to combine the input trees' support for a shared clade. One of "mean" (default), "max", "min". If None, the consensus' own clade-frequency support is kept and the input support ignored. TYPE: str | None DEFAULT: 'mean'

RETURNS	DESCRIPTION
PhyloNode	The constructed consensus tree.

Source code in src/piqtree/iqtree/_tree.py

def consensus_tree(
    trees: Iterable[PhyloNode],
    *,
    min_support: float = 0.5,
    support_aggregate: str | None = "mean",
) -> PhyloNode:
    """Build a consensus tree, defaults to majority-rule consensus tree.

    The min_support parameter represents the proportion of trees a clade
    must appear in to be in the resulting consensus tree.

    If min_support is 1.0, computes the strict consensus tree.
    If min_support is 0.0, computes the extended majority-rule consensus tree.

    By default the input trees' own support values are transferred onto
    matching consensus clades.

    Parameters
    ----------
    trees : Iterable[PhyloNode]
        The trees to form a consensus tree from.
    min_support : float, optional
        The minimum support for a clade to appear
        in the consensus tree, by default 0.5.
    support_aggregate : str | None, optional
        How to combine the input trees' support for a shared clade.
        One of "mean" (default), "max", "min". If None, the consensus'
        own clade-frequency support is kept and the input support ignored.

    Returns
    -------
    PhyloNode
        The constructed consensus tree.

    """
    if not 0 <= min_support <= 1:
        msg = f"Only min support values in the range 0 <= value <= 1 are supported, got {min_support}"
        raise ValueError(msg)

    if support_aggregate is not None and support_aggregate not in _SUPPORT_AGGREGATES:
        allowed = ", ".join(sorted(_SUPPORT_AGGREGATES))
        msg = f"support_aggregate must be one of {allowed} or None, got {support_aggregate!r}"
        raise ValueError(msg)

    trees = list(trees)

    if not _all_same_taxa_set(trees):
        msg = "Trees must be on same taxa set."
        raise ValueError(msg)

    newick_trees = [get_newick(tree) for tree in trees]

    consensus = make_tree(iq_consensus_tree(newick_trees, min_support))

    if support_aggregate is not None:
        _transfer_support(consensus, trees, _SUPPORT_AGGREGATES[support_aggregate])

    return consensus

Usage

For usage, see "Construct a consensus tree from a collection of trees".