Building a Phylogenetic Tree

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 choose the Actions ‣ Tree ‣ Build Tree item in the main menu.

You can also use the Tree Settings tab of the Options Panel:

Five methods for building phylogenetic trees are supported:

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