How to build a phylogenetic tree in Geneious Prime


Phylogenetic trees are used to infer evolutionary relationships among sequences.  Geneious can build phylogenetic trees using distance, maximum likelihood or Bayesian methods.  This guide describes the basic steps to build a tree and manipulate the tree viewer in Geneious.  

Before you embark on building your tree, you should familiarize yourself with the principles of tree-building and the strengths and weaknesses of each method.  The review below is a good place to start.

Molecular phylogenetics: principles and practice, Nature Reviews Genetics 13, 303–314 (2012).  doi:10.1038/nrg3186


1. Align your sequences

Before you can build a phylogenetic tree, you need to align your sequences.  To do this, select all your sequences and choose Align/Assemble - Multiple Alignment.  This link provides a guide to the available algorithms.  

Once you are happy with your alignment, select it and click Tree to open the tree building options. 

2.  Choose your tree builder and parameters

At the top of the tree building options you’ll see the available tree building algorithms.  This includes the built-in Geneious Tree Builder (and Consensus Tree builder), and any plugins you have installed.  


The Geneious Tree Builder produces distance trees using either Neighbor-Joining or UPGMA methods.  In addition, the following plugins are available for producing maximum likelihood, parsimony or Bayesian trees:

PHYML - Maximum likelihood

RAxML - Maximum likelihood, optimized for large datasets

Garli - Maximum likelihood

FastTree - Approximate maximum likelihood, for extremely large datasets

PAUP* - Parsimony or maximum likelihood (requires your own copy of PAUP*, either version 4.0b10, or 4.0a149 and above from here)

MrBayes - Bayesian analysis

More information on the maximum likelihood tree-builders is available at this link.

Each tree builder has a different interface for specifying the evolutionary model and other parameters.  We suggest you consult the user manual for each tree builder to familiarize yourself with the available options.  You may also wish to use a program like Modeltest outside of Geneious to determine the best model for your data prior to building the tree.


3. Run your tree

Click OK to start your tree building.  The time it takes to build the tree will vary depending on the algorithm you have chosen, the size of your alignment and the parameters (such as number of bootstrap replicates) you have chosen.  Distance trees normally complete fairly quickly (within minutes), but maximum likelihood and Bayesian trees may take hours or even days to run.


4. View your tree

When you tree has finished running, a new tree document will be created and it will automatically open in the viewer.  By default, Geneious displays trees in rectangular (rooted) layout, even if the tree is unrooted. Options for circular or radial formats can be found under the General tab, along with the Zoom controls.  


If you wish to root your tree, click on the node of the taxon you wish to specify as the outgroup and click Root.  To flip the position of taxa vertically, without changing the topology, use the Swap Siblings option.


The controls at the top of the viewer also contain options for coloring and setting the font sizes on your tree.  To color an entire clade, select the node at the base of the clade and select Color Nodes.


In the controls to the right of the tree viewer you can choose which field to display on the tips of the tree (e.g. Name, Description, Organism, Accession etc), and enable display of support values and branch lengths.   


To view the underlying alignment for the tree, click the Alignment View button above the viewer. Changes that are made in the Tree View will also be reflected in the Alignment View.  For example, if you color nodes in the Tree View, these will also be colored in the Alignment View.  The blue arrows next to the sequence in the Alignment View denote that these sequences are linked to the original source sequences.  This means that any changes made to the source sequences (e.g. editing the name) will be propagated to the alignment and the tree, and any changes made on the tree will be propagated back to the source. 


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