IDXL - tool for construction of a species tree from a set of incongruent gene trees. 
Discordance between the gene trees is modeled using ILS (Incomplete Lineage Sorting).
The method derives couplet based internode count and excess gene leaf count measures, 
from the input gene trees. These measures are used to form two different distance matrices, 
which are subsequently used to form a species tree. 
In process, a distance matrix based phylogeny reconstruction method 
such as neighbor joining is employed.

 Copyright 2015, 2016 Sourya Bhattacharyya and Jayanta Mukherjee.
 All rights reserved.

 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.

     * Redistributions in binary form must reproduce the above copyright
       notice, this list of conditions and the following disclaimer in the
       documentation and/or other materials provided with the distribution.

     * The names of its contributors may not be used to endorse or promote
       products derived from this software without specific prior written
       permission.

 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
 IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
 THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SOURYA BHATTACHARYYA OR JAYANTA MUKHERJEE
 BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.

 If you use this work or any portion thereof in published work,
 please email to us:
 
    Sourya Bhattacharyya:   <sourya.bhatta@gmail.com>
    Jayanta Mukherjee:	    <jay@cse.iitkgp.ernet.in>