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5.2. The tree, an abstract object
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When we speak of trees, of species,of phylogenetic trees, of course, it's a metaphoric view of a real tree. Our trees are abstract objects. Here is a tree and the different components of this tree. Here is what we call an edge or a branch. We have nodes, a particular nodeis the root and other nodes are the leaves here terminal nodesand we see that when we draw a tree as an abstract object, we put the root upside and the leaves downside so it's the reverse of a classical natural tree. We need an expression to describe a tree and we will use this kind of expression, how does it work? It uses parenthesis and you see that this means that part of the tree, this that part of thetree and then it's easy to see that, that part of the expression refers to this and the final expression refers to the whole tree. OK. A tree expression, we willuse this kind of expression when describing the execution of our phylogenetic tree or reconstruction algorithm. Of course it doesn't matter howthe tree is drawn, it could be like that with the same leaves and it is the same topology and so it is the same tree expression.
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