| Trees must be at the Newick format, without branch lengths. The leaves that are associated in both phylogenies must have the same name in both phylogenies. Trees must be fully resolved (no polytomies). Each leave in one phylogeny must have one and only one associated leave in the other. |
- Names of the leaves
If the leaves in your two trees have different names, they have to be changed
in order for the associated leaves in both trees to have the same names (Figure 1
below becomes Figure 2). Names of the
leaves cannot be numbers but can be any character string.
Figure 1
Figure 2
- Trees with different number of
leaves.
The two trees should have the same number of leaves. Leaves in one tree that
are associated with no leaf in the other tree should be removed. If one leaf in
one tree is associated with several leaves in the other tree, some leaves
should be pruned in the second tree or duplicated in the first tree. For
instance in the tree below (Figure 3), the leaf 4 is associated with three
leaves in the second tree (D, E and F). One can either
group the leaves D, E and F into a single leave or add two
leaves (5 and 6) in the first tree, with three possibilities
then: leaves 4 and 5, 4 and 6 or 5 and 6
as monophyletic groups. These choices will obviously impact on the result of
the degree of congruence and should be made considering the biology of the
species.
If you need more precisions, see the article in pdf or contact Damien de Vienne at damien.de-vienne@u-psud.fr.