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.

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 .

• Exclude masked sites. Excludes sites containing Masked annotations from the analysis without permanently removing them from your alignment. See section 12.2.1 .
• Genetic distance model. This lets the user choose the kind of substitution model used to estimate branch lengths. If you are building a tree from DNA sequences you have the choices “Jukes Cantor”, “HKY” and “Tamura Nei”. If you are building a tree from amino acid sequences you only have the option of “Jukes Cantor” distance correction.
• Tree building method. There are two methods under this option – Neighbor joining and UPGMA.
• Outgroup. Choose which sample to use as an outgroup, or leave it as “no outgroup” to build an unrooted tree.
• Resample tree. Check this to perform resampling.
• Resampling method. Either bootstrapping or jackknifing can be performed when resampling columns of the sequence alignment.
• Number of samples. The number of alignments and trees to generate while resampling. A value of at least 100 is recommended.
• Create Consensus Tree. Choose this to create a consensus tree from the resampled data.
• Sort Topologies. Produce trees which summarise the topologies resulting from resampling.
• Support threshold. This is used to decide which monophyletic clades to include in the consensus tree, after comparing all the trees in the original set.
• Topology Threshold. The percentage of topologies in the original trees which must be represented by the summarizing topologies.
• Save raw trees. If this is turned on then all of the trees created during resampling will be save in the resulting tree document. The number of raw trees saved will therefore be equal to the number of samples.