/pedigreeSim

PedigreeSim is software that generates simulated genetic marker data of individuals in pedigreed populations. A population can consist of either diploid or tetraploid individuals. PedigreeSim can simulate meioses with or without chiasma interference, and in tetraploids it can simulate meioses with two bivalents or one quadrivalent per set of hom(oe)ologous chromosomes. Also varying probabilities of preferential versus random pairing of chromosomes can be simulated, allowing to simulate amphidiploids as well as autotetraploids and intermediate forms.

Primary LanguageJava

PedigreeSim 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.

This program 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 St, Fifth Floor, Boston, MA 02110-1301 USA or obtain one at http://www.gnu.org

contact: address: R.E. Voorrips Wageningen University and Research - Plant Breeding P.O. Box 16 6700 AA Wageningen The Netherlands e-mail: roeland.voorrips@wur.nl

This distribution includes a copy of the jsci-core library which is subject to the following conditions:

JScience - Java(TM) Tools and Libraries for the Advancement of Sciences. Copyright (C) 2006 - JScience (http://jscience.org/) 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
  and include this license agreemeent. 
* 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.

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 THE COPYRIGHT OWNER OR CONTRIBUTORS 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.

A compiled version of the software is included in folder "compiled". See the ReadMe.txt file in that folder for instructions.