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PDAP:PDTREE:
A translation of the PDTREE application of Garland et al.'s Phenotypic Diversity Analysis Programs
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Peter E. Midford, Theodore Garland Jr., and Wayne P. Maddison
First released September 2002
Current release March 2008
Important Note
Recent versions of PDAP:PDTREE (1.05-1.11) will calculate statistics for characters that
have missing values. Unfortunately, although the statistics and plots for the univariate statistics
(e.g., 'screens' 1-8) have been tested and are believed to be correct, and starting in 1.09 the bivariate statistics (e.g.,
the text at the bottom of the text pane of'screens' 9-11) are believed to be correct, certain values, such as most FIC file columns and the contrast values that appear in the scatterplots of screens 9-11 are not known to be correct. We are are working on correcting these issues and hope to have a complete solution in the near future. We are currently testing this, but such values should
be treated with caution.
For the present version, 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
Documentation in MS word format available here.
Documentation in PDF format available soon.
News
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:
- 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.
- 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.
- Download the PDAP:PDTREE
package.
- 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".
- 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.
- 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 16 March 2008
Last update of this page 16 March 2008
