Hickory

Software for analysis of geographic structure in genetic data


Software

The software is currently available only for Windows and Linux. The Macintosh version you see below uses WineBottler to produce a binary for Mac OS X. See the additional notes below.

You can download the software in several forms:

  1. For Windows: You can download either a self-extracting executable that uses the standard Windows installer or a ZIP archive. The same files (including complete source code, if you select the "Full installation" option) will be found in both. We recommend using the self-extracting executable unless you encounter problems with it, because it will automatically install the program in your "Program Files" directory and create a shortcut in the "Start" menu.

    There are several setup options available. Unless you are interested in studying the code or trying to compile it yourself (you'll need wxWidgets, Paul's NEXUS class library, which is from his software page, MCMC++, and the Boost C++ Library for that), you don't need to do the full installation.

    hickory-setup-v1.1.exe
    MD5 sum c4ceea460b237a5e4feeed97458955ba

    hickory-v1.1.zip
    MD5 sum 9719f7d16280c124c78aab537850d2bb

  2. For Linux: You can download a gzipped tarball that includes a GNOME X11 executable (compiled and linked with GCC v4.0 on Fedora Core 4) and complete source code. The Ubuntu binaries should work on any recent Linux. They were built on Ubuntu LTS v10.04 on 21 June 2010. The other binaries may work on older versions of Linux. They were built under an old version of Fedora. (I don't remember which one now.)

    Copy the downloaded file to any convenient directory and extract with the command:

    tar -zxf hickory-1.1-ubuntu.tar.gz

    This will create a directory "Hickory" under the current directory. You'll find the executable in that directory. The "build" subdirectory contains the Makefile, the "src" subdirectory contains the C++ source and associated resources, and the "documentation" and "sample" subdirectories contain what you would expect them to contain.

    hickory-v1.1-ubuntu.tar.gz
    MD5 sum 831840e05f14798822f4e808e032240d

    hickory-v1.1.tar.gz
    MD5 sum f8e430d8c7fc4aee8750c216b3cb6556

  3. For Mac OS X: The Mac OS X version uses WineBottler to wrap the Windows executable with Wine (a Windows emulator) and the necessary libraries. It requires X Windows. I'm relatively new to Mac OS X, but my understanding is that versions earlier than v10.5 (Leopard) did not install X Windows by default. I've tested this binary on both v10.5 (Leopard) and v10.6 (Snow Leopard), but I don't know whether it will work on earlier versions with X Windows installed. I do know that the binaries will only work if you have an Intel-based Mac.

    Installation is straightforward. Just download the file below (ca. 300MB), double click on the icon, and drag Hickory-v1.1.app to your Applications folder (or anywhere else that's convenient). It will take awhile for the program to start up when you double click on it, because it first has to start up X Windows, but once it's running, it should behave almost the same way that it does on Windoze or Linux. You will have to scroll up on the folder tree a long way to find the main part of your disk.

    Hickory-v1.1.dmg

  4. Old versions: If for some reason you're interested in an older version, ZIP archives and tarballs starting with version 0.8 are available from the links below:

Acknowledgments

Complete acknowledgments are found in the documentation. The development of Hickory is supported, in part, by a grant from the U.S. National Institutes of Health.


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