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How to run PAUP in Mac OS X Tiger (under classic environment)

PAUP * 4.0 (Phylogenetic Analysis Using Parsimony (and Other Methods)) is a popular phylogenetic software.  If you’re in this field of work, you’ve likely have used it or have at least heard of it before.  If you want to use PAUP and you have an Intel Mac, you’ll have to resort to the command line version of the program.  This is because the GUI (Graphical User Interface) version of PAUP only runs in older Macs with PPC processors (i.e. G3, G4, G5).

The nice thing about GUI version of PAUP is you can print your trees as a PICT file and you can import it into Word and other Adobe programs to edit it and polish it for a publication.  In the GUI version, it is much easier and faster to set up your phylogenetic analyses compared to the command line version.  I think everyone will agree with me here.

My Mac is an Intel Mac (MacBook Pro).  Recently I decided to purchase an older G4 iMac (the one that looks like a flower pot) so I can run the GUI version of PAUP under the classic environment.  This post is about how I got PAUP up and running on this older Mac.  Trust me, it was not a walk in the park.  The information in this post may be useful to you if you choose to do this because who knows when the GUI version of PAUP will be released for Intel Macs (probably never in my opinion).

Important: If you want to use the GUI version of PAUP, you’ll have to purchase an older Mac with a PPC processor (not Intel).

Part 1. Installing the classic environment in Mac OS X Tiger

So my flower pot iMac came with an installation of Mac OS X Tiger but it did not have the classic environment installed.  The classic environment allows the execution of the GUI version of PAUP.  If your older Mac has the classic environment already installed, you can skip part 1.

The seller did not have any restore discs so I couldn’t install the classic support.  If you don’t the disc with the additional installation package for classic support, the steps below will show you, step by step, how to install the classic environment without that disc.

1.  Download the Netboot image at either MacUpdate or from Apple.  Save the NetBoot9.dmg file to your desktop.

2.  Double click on it.  Open the English folder.  Inside you’ll find the file called NetBoot.pkg. Ctrl click or right click on NetBoot.pkg and select “Show package contents”.

3.  Open the Contents folder, then the Resources folder.  Inside the Resources folder, drag the file called NetBoot.pax.gz file to your desktop.

4.  Double click on NetBoot.pax.gz and Mac OS X Tiger will decompress it into a folder named “NetBootInstallation”.

5.  To open this folder you need to modify the privileges.  To do this, Ctrl click or right click on it and select “Get Info”.  A window will pop up and at the bottom of this window, under “Ownership and permissions”, change the “You have” from “No Access” to “Read only”.

6.  Now double click on the NetBootInstallation folder to open it.  There are two image files there: Applications HD.img and NetBoot HD.img.  Drag the NetBoot HD.img to your desktop and double click to mount it.

7.  Inside the mounted NetBoot HD, you’ll find the “Applications (Mac OS 9) and System Folder.  Drag both of them to the root level of your Macintosh hard drive (next to your Applications, System, Library, Users folders).

8.  Unmount the NetBoot HD.img.  Drag the NetBoot HD.img and NetBoot.pax.gz files into the trash.

9.  Open System Preferences.  Then open the Classic preference pane.  Mac OS X should identify Mac OS 9 system folder and you can select it and start classic environment.

Side note: If your hard disk was formatted with the OS 9 drivers it may even boot the computer from it.  If you do get it to boot you have to log in using NBUser as the username and netboot as password.

10.  Classic will tell you that the version of Quicktime is outdated and need to be updated.  Go ahead and let the changes occur.

Side note: You may also download a more recent version of Quicktime for classic from and update to Quicktime 6.0.3 to stop the annoying message.

Part 2.  Notes on installing PAUP and tweaking it to made it play nicely in the classic environment

1.  Install PAUP (Altivec version) from your CD-ROM.  Launch it and put in your serial number (found on your CD-ROM case I think).  The program may ask you to install PAUP fonts.  You can download the PAUP font file from the PAUP website and place it in the Fonts Folder in System Folder.

2.  To make PAUP function smoothly in the classic environment, we have to do a few things.  Go to System Preferences, click on Network, select the built-in Ethernet and go to the Apple Talk tab.  Enable the Apple Talk.

3.  Open a sample nexus file and Execute it.  Do a brief Heuristic Search or a Neighbour Joining/UPGMA analysis.  Then go to Print Trees.  When you go to Print Trees you may get an error.  Click on the (multi-coloured) Apple Icon in the top left corner and go to Chooser.  Select the printer.  You should be able to to see printers either on the network or attached.  The mac doesn’t need to be constantly attached to the printer but if you set this once, you shouldn’t have to set up the printer everytime you re-launch the classic environment and PAUP.  Once you set the printer, you should be able to go to Print Trees without any error.

How to install BioEdit on a Mac running Mac OS X

BioEdit is a very popular sequence alignment editor.  It was written by Tom Hall and it was made only for Windows.  This tutorial will show you how to install BioEdit on a Mac without the use of Parallels Desktop or other virtual desktop software running Windows in the background.

You’ll first need to install Wine.

To install Wine on your Mac, you’ll need an Intel Mac and should follow David Baumgold’s guide on how to install Wine on Mac OS X (check the comments below.  Some users have had success while others had some problems).  Follow his guide until you finish Part 3 Install Wine using MacPorts.  Then return to this page.

Install BioEdit using Wine

To install a BioEdit program, first download the installer file.  (  It should end with .exe.  Save the BioEdit installer file in your user directory (it should show up on the Places in your Finder, below your Desktop icon, and shows up as a little house icon).

Open Terminal and run the installer through Wine by using this command:

$ wine setup.exe

XQuartz will open (if it isn’t already), and soon you will the installer. Click through it to install the program.

Install Winetricks

To make BioEdit work, you’ll have to do some additional installations.  In the Terminal window, type:

$ sudo port install winetricks
$ sh winetricks mdac27

The Terminal will open the webpage in your browser. Download the software from the website and put it in /Users/YOURNAME/Library/Caches/winetricks/mdac27

Then on the Terminal window type again:

$ sh winetricks mdac27

Run BioEdit

Now you are ready to launch BioEdit.  To run BioEdit, type in Terminal:

$ cd ~/.wine/drive_c/BioEdit
$ wine BioEdit.exe

Make an short cut for launching BioEdit (optional)

It would be nicer not having to go to the Terminal everytime you want to use BioEdit.  You can make a icon that you can put on your dock in order to launch BioEdit quickly.  Go to your Spotlight search at the top right corner and type “AppleScript Editor”.  Once the program opens, in the big blank space, copy and paste the following:

tell application "Terminal"
    do script "/opt/local/bin/wine ~/.wine/drive_c/BioEdit/BioEdit.exe"
end tell

Next, press the Compile button at the top of the window. The text should become colored. Try pressing the Run button to run your script and it should open BioEdit successfully.  Save your script.  You can give it whatever name you’d like, but be sure to select File Format: Application in the save options, and leave Startup Screen unchecked.  Open up the Finder, go to where you saved your script/app, and drag that file to your Dock. It should stay there, just like a real application.  Now you can click it to launch BioEdit quickly without having to type in the Terminal.