raxmlGUI Files

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                           raxmlGUI
               A graphical front-end for RAxML
                   version 1.5b1 (Mac), June 2015

Silvestro, D. & Michalak, I. (2012) raxmlGUI: A graphical front-end for RAxML. 
Organisms Diversity & Evolution 12, 335-337, DOI: 10.1007/s13127-011-0056-0
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General Info
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raxmlGUI version 1.5b1 has been tested under Mac (Intel 64bit; OS 10.10)
Windows (XP, 7), and Linux (Ubuntu) using Python 2.5-2.7.
The package includes executable files of RAxML 8.1.2 (Stamatakis, 2014). 


raxmlGUI does not support Python 3.



NOTES FOR MAC USERS:

Apple's recent security measures imply that programs from developers that are not
registered at Apple do not run on Mac computers by default. Typically, when you
try to run the program you get a message such as:

"the package is damaged and should be moved to the trash"

To be able to run the raxmlGUI app on your Mac you must change the System Preferences
to allow software from unidentified developers to run. 

On Mac OSX 10.9
1. Open System Preferences (available from the apple menu)
2. Open "Security & Privacy"
3. Change the setting to "Allow apps downloaded from: Anywhere"

On more recent MacOS versions
1. Control-click the app icon, then choose Open from the shortcut menu
2. Click Open
The app is now saved as an exception to your security settings, and you can open it in
the future by double-clicking it just as you can any registered app.

You can also grant an exception for a blocked app by clicking the “Open Anyway” button
in the General pane of Security & Privacy preferences. This button is available for about
an hour after you try to open the app.

To open this pane, choose Apple menu > System Preferences, click Security & Privacy,
then click General.

More information can be found at the Apple website.




Release Notes version 1.5b1
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This is a beta version! 

This version of raxmlGUI you can run your analyses (currently with limited
functions) using the CIPRES Science Gateway (Miller et al. 2011) via the
REST API (Miller et al. 2015). You will need to install the necessary
python toolkit, kindly provided by Terri Schwartz from the SDSC and
included in the package.

Further details are provided in the updated manual. For additional info,
suggestions, bug reports please contact us at raxmlgui.help@gmail.com.
You can download previous stable versions orf raxmlGUI at
http://sourceforge.net/projects/raxmlgui/files/.


Contacts
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Please report suggestions and bugs to:
	raxmlgui.help@gmail.com	

To receive updates notifications join raxmlGUI mailing list at:
	https://lists.sourceforge.net/lists/listinfo/raxmlgui-news


Known issues
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On Mac OS 10.6 unexpected crashes have been reported.
Work-around: a downgrade to Python 2.6 seems to fix the problem


Run raxmlGUI
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To run raxmlGUI on a Mac simply copy "raxmlGUI.app" to your Applications
folder and double click on "raxmlGUI.app". Note that, since version 0.93,
raxmlGUI is launched using AppleScript thus adapting to the Python version
you have installed on your machine (2.5-2.7). 

To run the Multi-platform release of raxmlGUI you can launch the file 
"raxmlGUI.py" with a double click (Windows), or browse through the Terminal 
to the program directory using

"cd ~/.../raxmlGUI1.3" 

and type

"./raxmlGUI.py" or "python raxmlGUI.py" (UNIX)

More details are provided in the Manual.