PedigreeSim is software that generates simulated genetic marker data of individuals in diploid and polyploid pedigreed populations.
A population can consist of either diploid or polyploid individuals. PedigreeSim can simulate meioses with or without chiasma interference, and in polyploids it can simulate meioses with bivalents and/or quadrivalents per set of hom(oe)ologous chromosomes. Also varying probabilities of preferential versus random pairing of chromosomes can be simulated, allowing to simulate allo- as well as autopolyploids and intermediate forms. Unreduced gametes generated through first division restitution (FDR) or second division restitution (SDR) can also be simulated.
Implementation
Input and output files are text files in simple tabular form that are easily produced or read by other software including Excel, R and other statistical packages.
PedigreeSim is written in Java, which means that it is available on any platform where Java is available, including among others all distributions and versions of Linux, Windows and Apple OS.
Licensing
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 (http://www.gnu.org); 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.
Source Code
Both source code and a compiled version of PedigreeSim is available at Github. The current version (2021) is v 2.1.
