Erik+2

Erik+2 has been implemented in C++ to be run in a UNIX terminal. Given an alignment of four nucleotide sequences, the file computes the scores and weights for each possible tree topology according to
http://sysbio.oxfordjournals.org/content/early/2015/11/11/sysbio.syv086.abstract

Download the compiled version:
Erik+2 for 64 bit processor (new version: March 8th, 2016)

To run Erik+2 type ./Erik2. You may have to change the mode of the file ("chmod u+x") in order to make it executable.

Input: The input asked by Erik+2 is a FASTA file containing the alignment, and an integer m=1,2,3 expliciting the number of mixture partitions to be considered.

Output: The output are the scores and weights provided by the method applied to the alignment. Each score / weight is computed according to one possible topology relating the sequences: 12|34, 13|24, 14|23.

Alternatively you can download the SOURCE CODE here.

IMPORTANT: To run Erik+2 it is necessary to have installed the C++ linear algebra library Armadillo http://arma.sourceforge.net/ which is needed to compute the singular values of some matrices.

When using this software, please cite

J. Fernández-Sánchez and M. Casanellas, Invariant versus classical quartet inference when evolution is heterogeneous across sites and lineages, Systematic Biology (2016), 65 (2), 280-291





Previous versions:
Erik+2 for 64 bit processor (old version: works under the assumption that species are given in alphabetical order. We are indebted to David Swofford for pointing out this).




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Copyright 2013, 2014, 2015 Casanellas and Fernandez-Sanchez.
Erik+2 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Erik+2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details, http://www.gnu.org/licenses/