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fineSTRUCTURE v2 & GLOBETROTTER

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      • fineSTRUCTURE

  • Software
  • Software: R tools
  • Detailed Manual

      • Data

  • Suitable Data
  • Phasing
  • Complex example

      • Methodology

  • Main paper
  • Population Clustering
  • What is a population?
  • GLOBETROTTER Admixture
  • SOURCEFIND Admixture

      • Other

  • Registration & Updates
  • Tools and Scripts
  • FAQs
  • Applications/Links

      • Authors

  • Daniel Lawson
  • Garrett HellenthalDaniel FalushSimon Myers
    • © 2012 Daniel Lawson.
    Website template by Arcsin
    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.

    Please consider Registering, if you have not already done so.

    NB Installation instructions are below: Linux and Mac OS X should work fully.

    What you need

  • FineSTRUCTURE v4 command line tools for your processing machine.
  • The 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 are (from version 4.1.0) nearly non-existent!
    • Linux:
      • GCC c++ compiler (package build-essential in ubuntu)
    • Mac OS:
      • GCC c++ compiler (package gcc in brew)
    Installation fs4 comes with an installation script fs_install.sh. This is optional but will help novices get the correct version for their computer as well as adding it to their PATH variable.

    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 depricated and provided 'as-is' with no expectation that it still works. You MUST USE the command line version above for the analysis! You can still access it here

    PERL ISSUES

    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

    We will do our best to support you if you are having installation problems.

    Please report all problems, 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.