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To build a tree from an alignment either press the Build Tree button on the toolbar, select the Tree ‣ Build Tree item in the alignment context menu or the Actions ‣ Tree ‣ Build Tree item in the main menu.

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     <img src="/wiki/download/attachments/4227492/Building Phylogenetic Tree.png"/>
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Also you can use Tree Settings tab of the Options Panel:

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     <img src="/wiki/download/attachments/4227492/Building Phylogenetic Tree_1.png"/>
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Three methods for building phylogenetic trees are supported:

1. The PHYLIP Neighbour-Joining method. The PHYLIP package implementation of the method is used under the hood.
2. The MrBayes external tool. Check MrBayes Web Site for more details.
3. PhyML Maximum Likelihood method. Check PhyML Maximum Likelihood Web Site for more details.

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