Treeduce

A preprocessing algorithm for Hybridization Number on any number of binary or nonbinary trees.


Reference

Leo van Iersel, Steven Kelk and Celine Scornavacca, Kernelizations for the hybridization number problem on multiple nonbinary trees. Under revision. Preliminary version in WG 2014. LNCS 8747, 299-311 (2014). arXiv.


Installation

Download the source file Treeduce.java.

Download and install a Java Compiler.

Open a terminal window and navigate to the folder of Treeduce.

Type “javac Treeduce.java” to compile the program.


Running the program

Type “java Treeduce input.tree [k] [-s]”

input.tree text file containing any number of trees in Newick format
k the value of the parameter (default is 1)
-s use this to enable silent mode

The reduced trees will be saved in Newick format to a file called “reduced.tree”.


 Example

An example input file: example.txt

 

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