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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Two 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.