TF-pipe

TF-pipe is a Perl pipeline to accelerate TreeFinder analyses manifold by running parallel jobs on clusters running the Sun Grid Engine. It runs several rounds of ML optimization as is described in Verbruggen et al. 2010 and Cocquyt et al. 2010.

Note: Gangolf has put support for multicore processors in the March 2011 version of Treefinder, so unless you want to run several rounds as described in the papers above, you're probably better off using the built-in multicore support.

This is for advanced users only; you will have to make changes to the code to get the dependencies right and change the program settings to suit your needs.

Downloads

tf-pipe.pl & modules v.1.01 download (zip file)

Notes and disclaimer

TF-pipe is in development and has not been tested extensively. It is quite plausible that incorrectly formatted input could lead to nonsensical output.

TF-pipe is open-source and distributed according to the GNU General Public License. The program is provided "as is" without warranty of any kind, either expressed or implied. The entire risk as to the quality and performance of the program is with you. Should the program prove defective, you assume the cost of all necessary servicing, repair or correction. The author will not be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the program (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs).