Consensus trees

Often, several and even many equally parsimonious trees are found. There is no objective way to choose one instead of the others. However, these trees may be very close to each other. For that, it is useful to compute consensus trees that shows the common structures among all trees.

The first option is to compute the strict consensus tree that keeps only the nodes belonging to all trees. The other nodes are destroyed and shown as polytomies.

The second option is to compute the majority-rule consensus tree that gives at each node the percentage of occurrence of this node among all trees. Usually, nodes below 50% are rejected and shown as polytomies, while nodes with percentages between 50 and 70% are not considered to be reliable. Above 80%, the node is considered as very robust.

The strict consensus tree is thus a majority-rule consensus tree showing only nodes with percentages of 100% and not less. In any case, recall that these consensus trees might gather incompatible trees, and only the physical interpretation may tell which is the most satisfactory one.

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