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

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

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How to Download

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 module runs inside of Mesquite.
3. Fill out our questionaire, below, and download the PDAP:PDTREE module.
4. 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".
5. 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.
6. 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.

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