PaintMyChromosomes.com
fineSTRUCTURE v4 & GLOBETROTTER

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© 2012 Daniel Lawson.
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Important Note: fs4 includes ChromoPainter, which have different licences and authors. Both are free for Academic use only, and explicitly exclude commercial applications. See the file COPYING in the download for details.

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NB Installation instructions are below: Linux and Mac OS X should work fully. There is very limited support for Windows (but full support if you use cygwin).

What you need

  • FineSTRUCTURE v4 command line tools for your processing machine.
  • FineSTRUCTURE GUI or R library for visualisation, on your local machine.
  • GLOBETROTTER for performing admixture dating. You will also need a separate ChromoPainter v2 for this analysis. (NB FineSTRUCTURE comes with a simplified version of ChromoPainter).
  • FineSTRUCTURE v4

    Current binary download. This includes the binary (mac/linux) for the command-line version of fineSTRUCTURE version 4 and all the important scripts. IMPORTANT NOTE: If you experience problems getting the binary to work, get in touch and we'll try to compile it differently to work in all environments.
    See the manual for usage - it is now really very easy for small datasets!

    Dependencies for the command line version:
    • Linux:
      • GNU Scientific Library (GSL, development version package libgsl0-dev and libgsl0 in Ubuntu, gsl-devel in OpenSUSE)
      • GCC c++ compiler (package build-essential in ubuntu)
    • Mac OS:
      • GNU Scientific Library (GSL package gsl in brew)
      • GCC c++ compiler (package gcc in brew)

    FineSTRUCTURE v2

    Old source code download. This is functionally very similar to the current v4 binary release but may during the transition period, try this if you experience problems with the binary.

    FineSTRUCTURE GUI

    IMPORTANT NOTE: The GUI is ONLY for visualising the result of the final FineSTRUCTURE stage. You MUST USE the command line version above for the analysis!
    Current source code download. This provides the GUI source code for Linux (somewhat cygwin/mac compatable, if you know what you are doing; see below).
    Windows Installer.
    Windows Zip file.

    fineRADstructure

    For use with RAD data, there is fineRADstructure, which can take in RAD data in a variety of formats for processing with fineSTRUCTURE.

    Installing FineSTRUCTURE GUI for Linux / source (GUI and Command line)


    Dependencies for the GUI:
    • GNU Scientific Library (GSL, development version as above)
    • automake (package automake in Ubuntu and OpenSUSE)
    • wxwidgets 3.0.0+ (packages libwxgtk3.0-dev and wx-common in Ubuntu, wxGTK-devel in OpenSUSE; WARNING: This has many dependencies.)
    • GCC c++ compiler (as above)
    Installation Instructions for the GUI:
    Assuming that you are continuing from a successful compilation of the command line version:
    tar -xzvf finestructure-0.1.0GUI.tar.gz # (check correct version)
    cd finestructure-0.1.0/gui
    ./configure
    make
    sudo make install # optional; installs finegui exceutable

    Installing FineSTRUCTURE GUI for Windows

    Windows users should use the installer above, which includes the GUI manual and example (linked from the program menu in "Finestructure GUI"). An executable version is provided in the zip file in case you don't have install permissions.

    You may also compile from source; you will need wxwidgets, a compiler such as MinGW and (optionally) a build environment such as Code::Blocks.

    Installing Finestructure GUI for Mac

    • Install wxwidgets: brew install wxwidgets
    • Download the latest version of the GUI from this page:
    • curl -O www.maths.bris.ac.uk/~madjl/finestructure/finestructure-0.1.0GUI.tar.gz
      tar -xzvf finestructure-0.1.0GUI.tar.gz
      cd finestructure-0.1.0/gui
      ./configure # make sure to use the default compiler here!
      make
    • Optionally, copy to your path: cp finegui ~/bin
    Requirements (thanks to John Didion!) using macports (or manual installation of these packages):
    • MacPorts from macports.org.
    • GCC: sudo port install gcc46
    • GSL: sudo port install gsl-devel

    Perl woes

    You may get a weird error when you use these perl scripts, starting with the line: Can't locate Switch.pm in @INC (you may need to install the Switch module) The solution is to install it! For Mac and linux, this is as easy as: sudo cpan -f Switch You get asked a lot of questions, which I answered with the defaults. I then had to run this line *again* and do source ~/.bashrc # which I symlinked to .bash_profile

    GLOBETROTTER

    See the GLOBETROTTER page for details.

    Further information

    Binaries for Linux can be provided on request but there is no guarantee we will be able to build for your environment. We will do our best to support you if you are having installation problems.

    Note that the software is currently in an early public beta; all problems should be reported, however minor. The fineSTRUCTURE software was written by Dan Lawson. It s published under a Non-free licence; note that this is a change from the previous version!

    For any queries regarding the software, please contact DL at: dan.lawson@bristol.ac.uk. Please consider Registering, if you have not already done so; the mailing list is a good place to get help.