Phylogenetic Trees in Geneious Prime

This video shows how to align sequences with the Muscle aligner, then build a phylogenetic tree in Geneious Prime using the built-in Geneious Tree Builder for distance trees, or plugins for maximum likelihood, parsimony, or Bayesian methods. Customize the tree layout, rooting, coloring, and displayed fields, and view how tree edits propagate back to the alignment and source sequences.

Introduction to Phylogenetic Trees

Align sequences, then build a tree in Geneious Prime using the built-in Tree Builder or a plugin for maximum likelihood, parsimony, or Bayesian methods. Set an outgroup, calculate bootstrap support, and customize the tree’s layout and display fields.
LENGTH 4 minutes

Recommended Resources

Phylogenetics FAQs

Common questions on building and manipulating phylogenetic trees in Geneious.

Does it matter whether I assign tree metadata to branches or to nodes?

Understand the effect of Assigning Support Values to Branches or Nodes.

How to display bootstrap percentages on a phylogenetic tree

Bootstrap percentages can be displayed when the Show Branch Labels option is selected.

Manual for Phylogenetic Trees

A guide to creating and using phylogenetic trees in Geneious.

More Geneious Academy

TUTORIALHow to Build Phylogenetic Trees in Geneious Prime
Build a phylogenetic tree from HIV and SIV sequences to trace which African primates HIV came from.
Read Tutorial
VIDEO SERIESMultiple Alignments in Geneious Prime
Choose the right alignment algorithm for your dataset size, from Muscle to MAFFT, then align multiple sequences and assess homology in Geneious Prime.
Watch Series
VIDEO SERIESMauve Alignment in Geneious Prime
Align whole or draft bacterial genomes with the Mauve plugin, order contigs against a reference, then convert the result for phylogenetic analysis.
Watch Series
VIDEO SERIESCreate Automated Workflows in Geneious Prime
Build a custom workflow in Geneious Prime from Sanger trimming to tree building, then scale it across document sets using parallel steps and branching.
Watch Series
Get started with Geneious today
Try Geneious FreePricing