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.