Tutorial 4

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BEAST Documentation->Tutorials->Tutorial 4

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Providing a user-specified starting tree

Users may specify a starting tree in Newick format:

Newick format

First create a newick element with an appropriate id (the tip labels in this tree must match the taxon ids in the taxa element):

	<newick id="startingTree">
		((((human:5.0,(bonobo:2.8, chimp:2.8):2.2):2.0, gorilla:7.0):5.0, orangutan:12.0):14.0, siamang:26.0);
	</newick>

Then ensure that the tree model element refers to your starting tree:

	<treeModel id="treeModel1">
		<newick idref="startingTree"/>
		<rootHeight>
			<parameter id="treeModel1.rootHeight"/>
		</rootHeight>
		<nodeHeights internalNodes="true">
			<parameter id="treeModel1.internalNodeHeights"/>
		</nodeHeights>
		<nodeHeights internalNodes="true" rootNode="true">
			<parameter id="treeModel1.allInternalNodeHeights"/>
		</nodeHeights>
	</treeModel>

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Alexei Drummond and Andrew Rambaut
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