Phylogenetic inference using PAUP* 4.0

Requires Geneious 6.0+

    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.

    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.