Phylogenetic tree analysis software

Align sequences, build and analyse phylogenetic trees using your choice of algorithm.

Built-in likelihood, distance and Bayesian phylogenetic tree building methods

The interactive distance matrix viewer allows you to rapidly calculate meaningful statistics for phylogenetics analysis.

Phylogenetic tree building and analyzing without juggling files

Simply select any alignment in Geneious Prime and your choice of algorithm to generate your phylogenetic tree with simple one click methods.

Your choice of phylogenetic tree building algorithms

  • 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
  • MrBayes – For Bayesian estimation of phylogenies, Geneious incorporates the MrBayes plugin which can be run on the local machine.
  • PAUP* – Launch the PAUP* plugin from inside Geneious 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 with the PhyML plugin
  • GARLI- Genetic Algorithm for Rapid Likelihood Inference
  • RAxML- Randomized Axelerated Maximum Likelihood
  • FastTree – Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences

Export your phylogenetic artwork and publish it

Manipulate the display settings to customize 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. Once your tree is built 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.

Introduction to Phylogenetic Tree Building in Geneious Prime


Building Phylogenetics Trees – Use Geneious Prime to analyze the evolutionary origins of human immunodeficiency viruses (HIVs) using molecular phylogenetic tools.

Plant Molecular Evolution – Annotate plant DNA sequences using BLAST and multiple alignment, then learn how to read a phylogenetic tree to explore genetic distance.

More Geneious Prime Features

AlignmentPerform pairwise and multiple alignments of DNA or protein using trusted algorithms, including MAFFT and ClustalW.

Assembly and MappingDe novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet.

Analysis and Annotation – Trim, assemble, annotate and view Sanger sequencing trace files

Molecular Cloning – View plasmid maps, automatically annotate vectors, find restriction sites; digest, ligate, and perform Golden Gate, Gibson, and Gateway cloning.

BLAST / NCBI – Connect to NCBI and PubMed, submit sequences directly to GenBank, BLAST sequences and search your own database.

Import Data – Import and convert common file types as well as their annotations and notes with a simple drag and drop

One of the absolute core advantages of Geneious is its seamless integration of industry standard phylogenetic software like MrBayes and PAUP*. Not only are they integrated, Geneious also adds a graphical interface that makes them very user friendly.  
Michael ForstnerTexas State University