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wxRAxML 1.0 (April 2011)
Graphical user interface for RAxML 7.2.8
by Jacek Kominek
Intercollegiate Faculty of Biotechnology
University of Gdansk-Medical University of Gdansk
jacek.kominek@biotech.ug.gda.pl
Original RAxML created by Alexis Stamatakis
(A. Stamatakis, Bioinformatics 22(21):2688-2690, 2006)
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Contents:
1) INTRODUCTION
2) INSTALLING WXRAXML
2.1) INSTALLATION UNDER WINDOWS
2.2) INSTALLATION UNDER UNIX/LINUX
2.2.1) REQUIREMENTS
2.2.2) BUILD USING CODEBLOCKS (graphical)
2.2.3) BUILD USING SCONS (command-line)
2.3) INSTALLATION UNDER MACOS
3) USING CUSTOM BUILDS OF RAXML
4) ACKNOWLEDGEMENTS & LINKS
5) SUPPORT & CONTACT
6) LICENSE
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1) INTRODUCTION
wxRAxML is a wxWidgets-based, cross-platform graphical frontend for the maximum-likelihood phylogenetic inference program RAxML created by Alexis Stamatakis. It is supposed to make it easier to run phylogenetic analyses with RAxML, which has a very wide palette of options and runmodes, which might be confusing and difficult to learn.
wxRAxML is a graphical user interface (GUI) and just that - it will create an appropriate command string and then run RAxML itself to do the job. It does not do any calculations or estimations on its own.
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2) INSTALLING WXRAXML
2.1) INSTALLATION UNDER WINDOWS
If you would like to build wxRAxML yourself on this platform, your best option is to use the CodeBlocks project file. You can get CodeBlocks at: (version 10.05 or above, preferably)
http://www.codeblocks.org/
In order to compile the program, you will also need the wxWidgets library, which you get at:
http://www.wxwidgets.org/
Once you have both installed, download the source distribution of wxRAxML and open the project file 'wxRAxML.cbp'. It will ask you to specify a 'wx' environmental variable, which should point to the root directory of your wxWidgets installation. Once you have set this up, it should compile without problems.
It should also be possible to compile it using the Windows version of Scons, but I have not tried it.
2.2) INSTALLATION UNDER LINUX/UNIX
2.2.1) REQUIREMENTS
wxRAxML relies on the wxWidgets-2.8.11 library to create the interface, so you need to have it installed on your machine prior to compiling it. You can either use a version distributed by your favourite distribution (search for 'wxGTK', which is the main linux build) or build one yourself, and place it in a location which can be found through the environmental variables.
2.2.2) BUILD USING CODEBLOCKS (graphical)
This is the recommended method to compile wxRAxML (and RAxML-7.2.8 which comes with it) on your machine. You should use the Codeblocks IDE version 10.05 or above, preferably. Open the file 'wxRAxML.workspace' and then run 'Build workspace' from under the Build menu, which should compile everything. If you would like to compile only wxRAxML itself, open the 'wxRAxML.cbp' file and then run 'Build' from under the Build menu.
2.2.3) BUILD USING SCONS (command-line)
Alternatively, if you prefer to use a command-line method to compile wxRAxML (and RAxML-7.2.8 which comes with it), you can use Scons version 2.0.0 or above, which is available in the repositories of all major distributions. Simply navigate to the folder where this readme file is located, and run 'scons' in the terminal to start the procedure.
If you don't have Scons installed or if you don't want to install it, you can run the standalone version bundled with wxRAxML by running the script 'scons.py' located in the root directory of wxRAxML.
Scons runs the 'wx-config' script to locate the wxWidgets files, and although it should work in most cases, it might have a problem in doing so if you have a custom installation of wxWidgets located somewhere outside the standard environment. Scons might complain about being unable to find wxWidgets headers or something along these lines. If this is the case, open the 'SConstruct' file in the root directory and look for this line:
env.ParseConfig('wx-config --cxxflags --libs')
Prefix 'wx-config' with the full absolute path of the root of your wxWidgets installation, where this script is normally located. If you don't know where your wxWidgets installation is, try 'locate wx-config' in the terminal, which should tell you the correct path. If it does not return any path, then you don't have wxWidgets properly installed, check the "ACKNOWLEDGEMENTS & LINKS" section for details where to find it, or use your distribution repositories (if using a Linux system).
2.3) INSTALLATION UNDER MACOS
Since the MacOS is a Unix-based system, in principle the same compilation procedure applies to it as to Unix/Linux. There are MacOS versions of CodeBlocks, Scons and wxWidgets available, the only downside is that you will need to compile wxWidgets yourself. The preferable method is to use Scons, with the above requirement that you will need to edit the 'SConstruct' file to indicate the path where you have installed wxWidgets.
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3) USING CUSTOM BUILDS OF RAXML
wxRAxML by default runs the SSE3-enchanced RAxML-7.2.8 executables from the 'raxml-7.2.8' subdirectory. If you would like to use a different RAxML build/version that you have built yourself, you need to place your own binaries in that directory for wxRAxML to use them. There is a filename caveat to it - a sequential RAxML build should be called 'raxmlHPC-SSE3' and the parallel build should be called 'raxmlHPC-PTHREADS-SSE3', as these are the filenames wxRAxML will look for. Your custom versions need not actually use the SSE3 extensions if your CPU architecture does not support them, but the binaries must be named this way nonetheless.
Several makefiles that come with RAxML-7.2.8 are also included in the package, so you can also build any version which you prefer, but keep in mind the above caveat.
Since wxRAxML is dedicated to desktop use, it currently DOES NOT support the MPI builds of RAxML, which are supposed be run on supercomputer clusters using advanced queueing systems.
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4) ACKNOWLEDGEMENTS & LINKS
wxRAxML would obviously not exist if RAxML weren't there in the first place, so a warm thank you goes to Alexis Stamatakis who made it, and whi kindly agreed to redistribute it's source together with this package.
wxRAxML is developped using CodeBlocks, which is a great free programming Integrated Development Environment (IDE). You can find it at:
http://www.codeblocks.org/
wxRAxML uses Scons (Software CONStruction tool) as one of its compilation methods. You can find out more about it at:
http://www.scons.org/
wxRAxML uses the wxWidgets library to implement a cross-platform interface. You can find out more about this great project at:
http://www.wxwidgets.org/
Last but not least, thanks go to SourceForge, which is a great community and a fantastic host for open software.
http://www.sourceforge.net/
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5) SUPPORT & CONTACT
wxRAxML is hosted at Sourceforge, you can find the latest version here:
https://sourceforge.net/projects/wxraxml/
If you have any comments, ideas, bug reports etc., please feel free to use the Sourceforge bug tracker or drop me a word at:
jacek.kominek@biotech.ug.gda.pl
Questions related to RAxML itself, its various features and options, should be directed to its author i.e. Alexis Stamatakis, rather than to me. You can reach Alexis's group at the following address:
http://wwwkramer.in.tum.de/exelixis/
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6) LICENSE
wxRAxML is distributed under the GNU General Public License v3 (GPL v3).
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