Phylogenetics in Geneious Pro™
Building a tree is just as easy as building an alignment. Without having to launch a new program you can just click on the alignment produced by any of the alignment algorithms in Geneious Pro™, then click the Tree button to begin. Geneious Pro offers a number of different methods for phylogenetic reconstruction.
Distance Methods
- Neighbor Joining – Use the fast and simple neighbor-joining methodology to build yourself a guide tree for large numbers of taxa in seconds
- UPGMA – Simple and fast hierarchical clustering method for phylogenetic reconstruction
Bayesian Methods
- MrBayes – For Bayesian estimation of phylogenies, Geneious Pro incorporates the MrBayes plugin which can be run on the local machine or sent to a supercomputer in New Zealand if you want to outsource the job via GreenButton
Maximum Likelihood
- PAUP* – Launch the PAUP* plugin from inside Geneious Pro through our streamlined GUI interface to perform Maximum Parsimony, Maximum LIkelihood. You must own or purchase a copy of PAUP* to use this plugin
- PhyML – Harness the fastest implementation of maximum likelihood from within Geneious Pro with the PhyML plugin
Additional Features
- ModelTest – Model-testing before phylogenetic estimation is a requirement for nearly all scientific publications, so ModelTest is integrated as part of the workflow for phylogenetic estimation using PAUP*
- Bootstrapping – Bootstrapping is implemented in all of the tree estimation methods inside Geneious with a click of a check-box
- Tree Viewing – Once your tree is built, view it in the interactive tree viewer, save it to a high quality vector format like svg, pdf or eps for publication or print it so you can stick it on the wall – all without switching away from Geneious Pro
- Tree Editing – Manipulate the display settings to add, remove or edit branch labels, node labels, end labels, tree shape, tree scale or color the clades to get your tree looking exactly the way you'd need it to
- Distance Matrices – The interactive distance matrix viewer allows you to rapidly calculate meaningful statistics in phylogenetics analysis
