Phylogenetic inference using PAUP* 4.0

PAUP* Plugin

Run PAUP* from inside Geneious to build trees using parsimony, distance matrix and likelihood methods. Modeltest is also included. You will need a licensed copy of PAUP* to use this plugin.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting a multiple sequence alignment and clicking on Tree in the toolbar. PAUP* is available as an option at the top of the Tree building options window.

Before building a tree you will need to set the PAUP* executable location to point to your copy of the command line version of PAUP* 4.0.


1.3.3 (22 Oct 2019) – Download

– Added a workaround for bug running modeltest with model scores from PAUP* alpha releases where parameter values were interpreted incorrectly

1.3.2 (02 Aug 2019) – Download

– Updated URLs for PAUP* alpha releases and manual

– Replaced modeltest for Mac OS with a 64-bit binary

1.3.1 (19 Jul 2017) – Download

– Fixed crash on Windows when running from a data directory containing certain non-Latin characters (e.g., Chinese)

– Support for alpha 153 and above

1.2.8 (09 Feb 2016) – Download

Bug Fixes:

– Fixed occasional failure when temp files are deleted before being read by PAUP*

– Made help text more descriptive and updated URLs

– Fixed rare bug that could lead to data loss when an error occurs during file writing

– Works with PAUP* version 4.0b10 or less, no alpha versions

1.2.6 (05 Jun 2013) – Download

Bug Fixes

– NJ ignoring specified model.

– Block panel not initialising with correct options

– Block panel not adding right lines when doing NJ modeltest.

– Crash when sequence has empty name

– Sets model after writing distance matrix to file for NJ and ML trees

1.2.4 (11 Apr 2012) – Download for Geneious 5.5

– Further changes to prevent the plugin freezing on large output


Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.

Note: Because there are a number of beta and test versions of the program you should mention the specific version of PAUP* somewhere in the methods.


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