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Construct a consensus tree from a collection of trees

A consensus tree can be constructed from a collection of cogent3 tree objects with consensus_tree. The method defaults to the majority-rule consensus tree - though different minimum levels of support can be used to achieve the strict consensus tree, and extended majority-rule consensus tree.

Usage

Majority-rule consensus tree

From a collection of trees, the majority-rule consensus tree can be constructed.

from cogent3 import make_tree
from piqtree import consensus_tree

tree1 = make_tree("(a,(b,(c,(d,e))));")
tree2 = make_tree("(a,((b,c),(d,e)));")
tree3 = make_tree("(a,((b,d),(c,e)));")

tree = consensus_tree([tree1, tree2, tree3]) # (a,(b,c,(d,e)));

Strict consensus tree

The min_support parameter can be set to 1.0 to construct a strict consensus tree (only the clades that appear in all of the trees). The parameter represents the proportion of trees a clade must appear in to be in the resulting tree.

from cogent3 import make_tree
from piqtree import consensus_tree

tree1 = make_tree("(a,(b,(c,(d,e))));")
tree2 = make_tree("(a,((b,c),(d,e)));")
tree3 = make_tree("(a,((b,d),(c,e)));")

tree = consensus_tree([tree1, tree2, tree3], min_support=1.0) # (a,(b,c,d,e));

Extended majority-rule consensus tree

When the min_support parameter is equal to 0, the extended majority-rule consensus tree is computed. 

from cogent3 import make_tree
from piqtree import consensus_tree

tree1 = make_tree("(a,(b,(c,(d,e))));")
tree2 = make_tree("(a,((b,c),(d,e)));")
tree3 = make_tree("(a,((b,c),(d,e)));")
tree4 = make_tree("(a,(c,(b,(d,e))));")
tree5 = make_tree("(c,(b,(a,(d,e))));")

tree = consensus_tree([tree1, tree2, tree3, tree4, tree5], min_support=0) # (a,((b,c),(d,e)));

See also