12.2 Tree building in Geneious Prime

To build a tree, select an alignment or a set of related sequences (all DNA or all protein) in the Document table and click the Tree icon or choose this option from the Tools menu.

If you are building a simple tree (Neigbour joining or UPGMA) using the Geneious tree builder, the tree can be built directly from a set of unaligned sequences, as the alignment will be built as part of the tree-building process. For more advanced trees, or if you wish to bootstrap your trees you must build an alignment first and use that as input for your tree. You can also select an existing tree document (which contains an alignment) and build another tree from that, as the alignment will simply be extracted from the existing tree and used build the new tree.


Figure 12.2: Tree building options in Geneious Prime

The following options are available in the tree-building dialog for the Geneious tree builder. For more information on these options see sections 12.3 to 12.4 .

   12.2.1 Using alignment masks