Genesis: PCA and Admixture plot viewer and publication quality image generator

    Genesis can be used to display screen and publication quality pictures of population PCA and admixture charts and has been developed by: Wits Bionformatics, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg

    Why use Genesis?

    Genesis takes the output of popular programs such as Admixture and EIGENSTRAT and produces good quality pictures, which the user can interactively change. There are first class tools that can be used to create good quality pictures, but they require expertise to use and best used when one already knows exactly what the output should look like. In practice there is a huge need for an interactive tool. Which PCs display interesting data can be interactively explored. Which colours are best to use is not just an aesthetic problem: in some cases a set of colours works well but with other data the same colours doesn't because the colours don't clearly contrast with a new position of the objects being drawn. There may be a need to rearrange the labelling or the data. We want to make the fonts as big as possible, but what is "big as possible" depends on the quantity and arrangement of data. Often when displaying admixture charts, multiple charts are shown in one diagram, we need to to keep consistency of colours and may want to play with the ordering of data.

    We see the need for an interactive tool that can be used to explore possibilities and produce good quality data. Although tools like Distruct and R are more flexible and produce very high quality pictures, Genesis is interactive and requires much less expertise to use.

    Requirements:

    Genesis requires Java 1.7 with SWT libraries installed. Genesis runs on Windows, Linux and MacOS X.  For Mac OS X, X11 must be installed. (Download XQuartz here)

    On Windows and Linux, the program should be run as:

    java -jar Genesis.jar

    On Mac OS X, X11 must be installed and the program should be run as:

    java -XstartOnFirstThread -jar Genesis.jar

    Some sample data files can be found here

    Download: The executable can be otained from here (Latest version:0.2.5 27 January 2015)

    GIT hub:  https://github.com/shaze/genesis
    From the command line: git clone https://github.com/shaze/genesis

    Documentation: The manual is available as a pdf file


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