Gene Stacker is a flexible tool for marker-assisted gene pyramiding. It can be used to construct efficient crossing schedules that gather desired alleles residing in multiple individuals into a single, specific target genotype (the so-called ideotype).

Given a set of initial (phase-known) genotypes, the desired ideotype and the genetic map of the crop, Gene Stacker approximates the Pareto frontier of crossing schedules with minimal number of generations, population size and linkage phase ambiguity, that create the ideotype starting from the available parental genotypes.

Several heuristics are provided, which yield different tradeoffs between solution quality and speed and allow to solve more complex gene stacking problems within reasonable time.

Stable releases are available for download at the Gene Stacker website. Changes in new releases are listed in the CHANGES file.

Assuming the availability of Maven, Java and a JDK installation, building Gene Stacker from source code should be as easy as running

mvn package

from inside the Genestacker root directory

|-- Genestacker
  |-- Genestacker-cli
  |-- Genestacker-lib
  |-- pom.xml
  |-- ...

This will create a jar package genestacker.jar, including all dependencies, in a bin subdirectory.

A simple R interface genestacker.R is included in the root directory

|-- Genestacker
  |-- genestacker.R
  |-- ...

that can be used to run Gene Stacker from R. This script depends on genestacker.jar which should be available in the same directory or in a bin subdirectory, where it is created after running mvn package.

For documentation and examples of how to use Gene Stacker, see http://genestacker.ugent.be. Running

java -jar bin/genestacker.jar -help

prints brief usage information including an overview of all possible parameters.

Gene Stacker is licensed under the Apache License, Version 2.0, see LICENSE file or http://www.apache.org/licenses/LICENSE-2.0. Copyright information is stated in the NOTICE file.

Gene Stacker is developed and maintained by

• Herman De Beukelaer (Herman.DeBeukelaer@UGent.be)