QGAStation 2.0

Software for the classical quantitative genetics

Copyright 2011 © 

Developed by Guobo Chen , Futao Zhang, Zhixiang Zhu, Xu Yang and Jun Zhu

Institute of Bioinformatics, Zhejiang University, China

Features of the Software
This software has several features: Handle complicated genetic models for agronomic traits, seed traits, and developmental traits; Analyze unbalanced data; Combine jackknifing techniques to test the significance of each genetic parameter; Some important references are listed in the result files.
The Graphic User Interface for Windows was developed by Guobo Chen.The GPU computing model was developed by Futao Zhang in MSRA. And the The Graphic User Interface for Macintosh was developed by Zhixiang Zhu.
What's New in QGA2.0
1. GPU was supported.
2. REML, BLUP were implemented.
3. MacOS version was released.
System Requirements
Operation System: Windows  XP, Windows 7 and Mac OS.
Download and Installation
   Downloads (for Windows 7, VISTA, Windows XP):
32-bit                                 64-bit
   Downloads (for Mac OS X):
x86_64
Unzip the downloaded file, and run the .zip file.
How to run the program

Eight steps to run an input file

1.Install CUDA driver  If your system is equipped with one or more NVIDIA CUDA-compatible devices and you want GPU computing, you should install CUDA driver to make the software run on GPU.The CUDA driver must be verison 270.81 (or greater) for Windows systems and version 4.0.50 (or greater) for Mac OS.

2.Install Microsoft Visual C++ 2010 Redistributable Package If Visual Studio 2010 is not installed in your Windows system, you should install visual c++ 2010 redistributable package to run QGAStation 2.0. For x64 systems, download and install vcredist_x64.exe. For x86 system, download and install vcredist_x86.exe .

3.Create an input file Regular text file editors, include the QGAStation can be used for preparing input files. But using Microsoft Excel, or other electronic table software can make it much easier to prepare and manage your input files. Each method employs different file formats. You could find data formats definition in the help document of each method, and we also provide some samples of input files under the Sample folder. Missing data is denoted by dot (".").

4.Open an existent files You could open an input file through main menu [File]>>[Open], or click [Open] icon on the toolbar to open a file including raw data.

5.Select analysis method and model An input file should be analyzed by a model using appropriate statistical methods. Select a model through menu [Method], which lists different methods collected in QGAStation, including Agronomy methods, Animal methods, Seed methods, Trial methods and Link Map method. Click one of selection in Method menu, a submenu  will pop out, which lists various models along with a certain statistical methods. Now, you could select a method and a model you want from the submenu.

6.Coefficient setting A Coefficient-setting Box will pop out when you have selected a certain model from [Method]. You could find the details about meaning of each coefficient in  help documents of every model selected.

7.Run After setting the coefficients, you could Run the input data with set coefficients through Run button at the bottom of Coefficient-setting Box, or exit the Coefficient-setting Box without running through click the Cancel button ,which also is at the right of the Run button.

8.View the result files The result files will be saved under the same direction of input file. Because all result files are text files, you could view the result files with any kind of text viewer, of course, electronic table software such as Microsoft excel is much better to view the result files .In every result file, data are separated by commas in every line.