Chapter 12
Building Phylogenetic Trees

Geneious Prime provides inbuilt algorithms for Neighbour-joining (Saitou & Nei 1987) and UPGMA (Mitchener & Sokal 1957) methods of tree reconstruction, which are suitable for preliminary investigation of relationships between newly acquired sequences. For more sophisticated methods of phylogenetic reconstruction such as Maximum Likelihood and Bayesian MCMC, external plugins for specialist software are available (see section 12.3.5 for a full list). These can be downloaded from the plugins page on our website or within Geneious by going to Plugins under the Tools menu.

  12.1 Phylogenetic tree representation
  12.2 Tree building in Geneious Prime
   12.2.1 Using alignment masks
  12.3 Tree building methods and models
   12.3.1 Neighbor-joining
   12.3.2 UPGMA
   12.3.3 Distance models or molecular evolution models for DNA sequences
   12.3.4 Distance models or molecular evolution models for Amino Acid sequences
   12.3.5 Advanced Tree Building methods
  12.4 Resampling – Bootstrapping and jackknifing
   12.4.1 Consensus trees
   12.4.2 Creating a consensus tree of existing trees
   12.4.3 Sort topologies
  12.5 Viewing and formatting trees
   12.5.1 Current Tree
   12.5.2 General
   12.5.3 Layout
   12.5.4 Formatting
   12.5.5 Show Tips, Node and Branch Labels
   12.5.6 Automatically collapse subtrees
   12.5.7 Show scale bar
   12.5.8 Statistics
   12.5.9 The Toolbar