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PDAP:PDTREE: A translation of the PDTREE application of Garland et al.'s Phenotypic Diversity Analysis Programs

Peter E. Midford, Theodore Garland Jr., and Wayne P. Maddison

First released September 2002
Current release November 2011

Important Note

Recent versions of PDAP:PDTREE (1.05-1.16) will calculate statistics for characters that have missing values. When there are no missing values, all statistics have been tested and are, to the best of our knowledge, correct. When there are missing values, the statistics for screens 1-8 and the bivariate statistics listed at the bottom of the text pane of 'screens' 9-11 have been tested and are believed to be correct. Likewise, the first 5 columns of FIC files have been tested and are believed to be correct.

Unfortunately, certain values, such as later FIC file columns and the contrast values that appear in the scatterplots of screens 9-11 are not known to be correct. We are continuing to work on correcting these issues and hope to have a complete solution in the near future.

If these values are of concern to you, you can always prune your tree down to the number of tips for which you have complete data for two given traits, and save the file. Analyses with contrasts should then be correct for those two traits.


Documentation in MS word format available here.

Documentation in PDF format available soon.


2 Novemeber 2011 Version 1.16 released. This version fixes a bug in the Grafen (1989) branch length transform.
3 August 2010 Version 1.15 released. This version includes several updated messages related to resolution of polytomies and integration with the new install system.
25 November 2008 Version 1.14 released. This version introduces a flag to ignore tritomies at the root, which are produced by some tree inference programs, updates the guided tour and other examples, adds character names to diagnostic chart axes, and improves support for writing distance matrices. Thanks to Wayne Maddison suggesting and contributing to these enhancements. This release also incorporates a bug reported by David Maddison when loading a nexus file that had been saved with screen 9 showing.
30 July 2008 Version 1.13 released as bug fix. This fixes some problems with scaling in screens 9A and 9B.
3 July 2008 Version 1.12 released. This version supports Mesquite 2.5. Most screens support the "Step Through Trees..." command. Any remaining chart scaling issues with screens 9A and 9B (the root reconstruction and regression screens) should be resolved.
11 March 2008 Version 1.11 released as bug fix. There are currently problems with the PDAP support for the 'phone home' version checking, we are working on a solution for these.
16 December 2007 Version 1.1 released as bug fix and minor enhancement.
21 September 2007 Version 1.09 released for Mesquite 2 compatibility and as bug fix.
19 January 2007 - Version 1.08(2) released as bug fix.
17 December 2006 - Version 1.08(1) released as bug fix.
15 December 2006 - Version 1.08 for Mesquite 1.11 and up released. Numerous bug fixes and the ability to change the degrees of freedom on screen 9 have been added. The later allows calculation of a polytomy corrected p-value for the regression on this screen. Note that the raw t and F values are correct and not affected.
19 October 2005 - Version 1.07(1) released as bug fix.
26 August 2005 - Version 1.07 for Mesquite 1.04 and up released. CI Files and several new scripting commands added along with two important bug fixes for exported files.
8 March 2005 - Version 1.06 for Mesquite 1.04 and up released. Bug fixes and enhancements to PDI file exporting.
31 October 2004 - Version 1.05 for Mesquite version 1.04 and up released. Several bug fixes.
23 May 2003 - Update for 0.995 released. Fixed error in sign-test calculation.
18 February 2003 - Provide a way to avoid reentering user info on this page.
28 January 2003 - Minor update - some changes for Mesquite 0.993 and web pages.
26 November 2002 - Source (java) is now available on the download page.
15 November 2002 - Update with several bug fixes.

How to Download

To download and install this package, do the following:
  1. If you have not already done so, install the most recent version of Mesquite. This may require installing java if your computer does not already have java loaded. To install mesquite, follow the instructions here.
  2. If you have not previously used Mesquite, we recommend spending some time exploring it before loading PDAP:PDTREE. This is because the PDAP:PDTREE package runs inside of Mesquite.
  3. You can install PDAP with the new Mesquite install system. Start Mequite and activate the item on the File menu titled "Available to Install or Update."
    1. If PDAP:PDTREE appears on the dropdown that appears, just select PDAP:PDTREE from the dropdown.
    2. Otherwise select the "Check Now for Notices/Installs..." In the dialog that appears, enter the following URL: http://mesquiteproject.org/pdap_mesquite/install.xml.
    The installer will put the program files for PDAP in the appropriate place in the Mesquite installation and then prompt you for where to put the PDAP examples folder. Place this anywhere that is convenient.
  4. If you have difficulties with the installer, please connect me at the email address listed at the bottom of the page. Meanwhile, you can download the PDAP:PDTREE package (see list below) and install manually.
  5. Uncompress the file (called pdap_bin) to create a folder (aka directory) called PDAP. This folder, in turn, will contain two folders, one titled "Put in mesquite directory", the other titled "Pdap examples". Within your Mesquite installation there is a folder titled "Mesquite_Folder." Within the "Mesquite_Folder" is a folder called "mesquite". This later folder is where you should move (e.g., drag) the folder called "pdap" which is in the "put in mesquite directory" folder. Do not put the whole "Put in mesquite directory" folder into "mesquite".
  6. You can put the "Pdap examples" folder into the examples folder in the "Mesquite_Folder" if you wish, but the examples don't need to be moved anywhere in particular. Within the examples folder are two folders, one containing the guided tour, the other containing several example files and PDI files. To try the tour, open the file called Part1.nex in Mesquite.
  7. To import a PDI file, just open the file from the File menu in Mesquite. Mesquite will display a list of formats it can translate. PDI should appear near the bottom of the list.

PDAP for Mesquite 2

Download PDAP in OSX format here
Download PDAP source in OSX format here

Download PDAP in Windows format here
Download PDAP source in Windows format here

Download PDAP in Linux/BSD format here
Download PDAP source in Linux/BSD format here

PDAP for Mesquite 1.1

Download PDAP in OSX format here
Download PDAP source in OSX format here

Download PDAP in Windows format here
Download PDAP source in Windows format here

Download PDAP in Linux/BSD format here
Download PDAP source in Linux/BSD format here

For general Mesquite questions contact Wayne Maddison.
For questions related to the DOS version of PDAP contact Ted Garland.

For questions about this package contact Peter Midford: peteremidford@yahoo.com.
Please put PDAP in the subject line.

Last update of PDAP:PDTREE 2 November 2011
Last update of this page 2 November 2011

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