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QDist

QDist implements a sub-cubic algorithm for computing the quartet distance between between general trees (i.e. the trees are not required to be binary).  An implementation of a faster algorithm for computing the quartet distance between binary trees is available here.

Download

qdist-src-2.0.zip

Prerequisites

You will need g++ from gcc installed on the machine. Furthermore you will need a BLAS library. On some Linux distributions one such comes pre-installed. On Ubuntu it can be aquired through the package manager. On Mac OS X system it comes pre-installed. You will also need the program CMake, which is used for build management.

Installation

Unpack the source code. In the src directory run:

$ cmake .

$ make

To confirm everything works as expected you can also run:

$ make test

To install the binary 'qdist' into your bin directory you can run:

$ sudo make install

or copy the binary 'qdist' to a directory of your choice.

Usage

After successful compilation you should have the binary file 'qdist' in the src directory. To run the program, provide two text files with trees described in the Newick format, e.g:

$ ./qdist testdata/small1.tree testdata/small2.tree

The program outputs the quartet distance along with other summary statistics. To get a overview of the output, run

$ ./qdist

Contact

Christian N. S. Pedersen, Bioinformatics Research Centre, Aarhus University

Comments on content: 
Revised 2012.03.13

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