/*

    MODER is a program to learn DNA binding motifs from SELEX datasets.
    Copyright (C) 2016, 2017  Jarkko Toivonen,
    Department of Computer Science, University of Helsinki

    MODER 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 2 of the License, or
    (at your option) any later version.

    MODER 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.

    You should have received a copy of the GNU General Public License along
    with this program; if not, write to the Free Software Foundation, Inc.,
    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

*/
bool use_markov_background=false;
bool use_positional_background=false;
bool use_two_strands=false;
bool use_pseudo_counts=true;
bool use_submotif=false;
bool use_em=true;
bool reestimate_error_rate=true;
bool use_logodds_score=true;
bool print_alignment=false;
bool count_palindromes_twice = false;