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easyRAx

*New 2010-04-07* Version 1.3.1 - Download here. This is the new version for RAxML v7.1.0 and above.

Version 1.2 - Download here. This is a legacy version and will only work with RAxML v7.0.4

This is a small wrapper script for the program RAxML. RAxML is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. RAxML is available from here.

The script aims to make execution of RAxML a little easier by use of simple command-line menus and some user input.

The script relies on a few assumptions, these are:

  • You are running linux, the tool was developed under Ubuntu. Sorry no Windows or Mac * at this time,
  • The programming language PERL is installed,
  • RAxML** is compiled and copied to the /usr/bin/ directory or a similar all environment path,
  • You run the easyRAx script from the easyRAx folder,
  • Your sequence files are within a folder under the easyRAx folder,
  • You don't wish to compute anything more complicated than with the options available to the 'Fast & Easy' or 'Hard & Slow' methods described in the RAxML manual.

To run the script, simply navigate to the easyRAx folder in your Terminal window and run perl easyRAx.pl.

Some code has been adapted from perl-scripts available on the RAxML homepage without permission, however, I hope that the authors will not take exception to this as it was done with the best of intentions. This has been reflected in the scripts comments. :)

** Please make sure that if you have a multi-core machine you compile the RAxML-PTHREADS version as well as the normal version and place them both in the /usr/bin/ folder.

* A recent test showed that easyRAx does indeed run on a Mac. It was tested with OSX 10.4.1 but should run on all newer versions of Mac OSX. NB - The "Guide to install RAxML on MACs" was used and may need to be followed for easyRAx.

Creative Commons License
easyRAx by Guy Leonard is licensed under a Creative Commons Attribution-Non-Commercial-Share Alike 3.0 Unported License.

 
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