Tutorial 4.1

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BEAST Documentation->Tutorials->Tutorial 4.1

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Providing a UPGMA starting tree

Users may specify a UPGMA starting tree by adding the following XML about the treeModel:

	<upgmaTree id="startingTree" usingDates="false">
	 	<distanceMatrix correction="JC">
			<patterns idref="patterns1"/>
		</distanceMatrix>
	</upgmaTree>

NOTE: if you are preforming an analysis on time-stamped data then you should set usingDates="true".

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

	<treeModel id="treeModel1">
		< upgmaTree 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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