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Extra CLUES for uncomfortable Mac OS X users
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ASSUMPTIONS
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You have downloaded an unpacked the latest version of AutoDecay.
You have read the README.txt and HelpText.txt files.
You do not have a working knowledge of Unix/Linux.
You have located and started a Terminal (in the Utilities folder inside your Applications folder).
Note that Perl is already installed on Mac OS X. No need to install that!

HOW TO GET AUTODECAY INSTALLED PROPERLY
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1. The terminal starts up in your home direcory.
Supposedly, the autodecay folder has been extracted somewhere. On your Desktop, say. If the autodecay folder is elsewhere, move it there first to make this work as easy as possible.

2. Here's how to set things up to run smoothly. Type the following commands, ending each with Enter. Type the commands EXACTLY like this with spaces, periods and all. 

mkdir bin
mv Desktop/autodecay/UNIX/AD.pl ./bin
mv Desktop/autodecay/UNIX/AD.def .AutoDecay
chmod +x bin/AD.pl

3. Type the following command in the terminal window

echo $SHELL

If the output is "/bin/bash", type the following command:
echo "PATH=$HOME/bin:$PATH; export PATH" >> .profile

If the output is "/bin/tcsh", type the following command:
echo "setenv PATH {$HOME}/bin:{$PATH}" >> .profile

4. Now close your terminal window. This completes the installation of AutoDecay. You only need to perform the installation once.



HOW TO GET AUTODECAY RUNNING
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1. Open a new terminal window. 

2. I have no idea where your tree file is. Use the "cd" command (change directory) in the new terminal to move to the folder where the tree file is. Let's say it is in a folder "Research" and inside a folder "Support" within the Research folder. Then you would use the cd command like this:

cd Research/Support

3. The tree file MUST be a native text file. If you used a Windows or Mac Classic (i.e. before OS X) version of PAUP* or any other Windows or Mac Classic program to create it, the file has to be fixed. 

If this is the case (or just to play it safe), open the file in PAUP*'s editor; select "save as" and click options before saving, selecting unix. You only need to do this once for a file.

Note: Instead of doing the editor thing you can use the commands below.
Tree file from Mac Classic:
tr "\r" "\n" < tree_file_name > new_tree_file_name

Tree file from Windows:
tr -d "\r" < tree_file_name > new_tree_file_name

4. Now you are ready to run the first AutoDecay step: Setup. Type the following (substituting tree_file_name for your file name of course):

AD.pl -s tree_file_name

5. Start PAUP* as you usually do and excute your DATA file. Then execute the file that  ends with ".adc" which was created by AutoDecay. You can check the contents of the current folder by typing the "ls" command in the terminal.

6. When all analyses has been completed in PAUP*, extract your decay values. (You need the optimal tree length available as the last parameter)

AD.pl -e adc_file_name optimal_tree_length

7. Done. Open the tree in TreeView to display the decay values.