General description

AlphaSim is a software package for simulating sequence, genotypic, phenotypic, and pedigree data in a wide range of population types (e.g., animal breeding, plant breeding, human genetics, natural populations). In developing AlphaSim major emphasis was placed on flexibility, computational efficiency, and ease of use. Populations can have almost any pedigree structure, almost any type of selection, a wide range of genotyping platforms, and multiple traits with a wide range of alternatives for genetic architecture. Additionally, AlphaSim also includes features for genome editing, manipulating the recombination rate and its genetic architecture, performing optimal contribution selection, and other “tricks”.

Any questions? go to AlphaSim Forum and join the discussion.


Download

1. User Manual

Click here to see the html version.

2. Binaries for Linux, Mac and Windows

The AlphaSim1.08 folders contains:

  • 7 programs (AlphaSim, MaCS, alphaformatter, AlphaBayes, AlphaBayesP, AlphaAGH and AlphaMate),
  • 1 pdf (AlphaSim User Manual),
  • 1 parameter file (AlphaSimSpec.txt),
  • 1 seed file for randomisation (Seed.txt),
  • A folder containing examples.

Running AlphaSim requires AlphaSimSpec.txt, MaCS2  (Chen et al. 2009), and alphaformatter. MaCS and alphaformatter are called from within AlphaSim if the program is started from the first generation. In contrast, AlphaBayes, AlphaAGH and AlphaMate are called only when specific options are activated. Further details are given in the user manual.

In addition, we supply a Microsoft Excel sheet (MaCS_parameters.xlsx), which can be used to compute the values of the parameters included in the RunMacs.sh file, as well as six exemplary RunMacs.sh files for different species (cattle, rabbit, maize and wheat). Further details are given in the user manual.


2 We thank Gary Chen for allowing us to redistribute his MaCS and msformatter executables alongside our AlphaSim executables.


3. AlphaSim Version 1.08 (March 2017)



 


AlphaSim GUI

In an effort to improve the accessibility and usability of our AlphaSim software, we have developed a graphical user interface (GUI), which uses the Java runtime environment (JRE).   By increasing the usability of our software, we hope that the impact of these programs will be even greater, especially for people where available resources are at a premium.

Download

AlphaSim Gui Version 1.08 (March 2017)

Tutorial Video



Previous versions

Version 1.07 (March 2017)
Version 1.06 (October 2016)
Version 1.05 (May 2016)
Version 1.04 (December 2015)
Version 1.03 (November 2015)
Version 1.02 (October 2015)
Version 1.01 (September 2015)
Version 1.00 (February 2015)