The software provided here calculates a tree of population relationships based on nucleotide sequence or restriction site data for individuals from a set of populations. The software was originally written and released in 1996 and has not been updated since 1998. It uses a command line interface, but I hope it is not too difficult to use. The documentation is sparse, so if you have problems using the software, please feel free to contact me.
I hope eventually to incorporate the Nucleodiv analyses into Hickory, although when I do so they will undoubtedly have a Bayesian flavor. If you are interested in that possibility, keep an eye on the Hickory website for announcements.
The software is currently available only for Windows and Linux.
You can download the software in several forms:
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. I 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 (but it is a DOS mode program).
Two binary files are required for proper execution of the program, the main program file (specificity.exe) and a dynamic load library (cygwin1.dll). Unless you're familiar with the Cygwin tools, I recommend that you install both of these files to the same directory.
setup.exe (self-extracting executable)
nucleodiv-1.7.zip (ZIP archive)
For Linux: You can download a gzipped tarball that includes an executable (compiled and linked with GCC v3.2.1 on RedHat v7.2) and complete source code. Copy the downloaded file to any convenient directory and extract with the command:
tar -zxf nucleodiv-1.7.tar.gz
This will create a directory "specificity" under the current directory in which you'll find the executable and a subdirectory "src" of that directory in which you'll find the C++ source, Makefile, and associated resources.
nucleodiv-1.7.tar.gz (gzipped tarball)
This code is provided free of charge, but I have inserted a copyright notice in each of the files. That means that you are free to distribute this code to your friends or post it on a BBS or anonymous ftp site provided:
1) You do not charge for it, except to recover the cost of distribution.
2) You distribute *all* of the files included in this distribution AND do not distribute any changes you make to the source files.
I have done my best to ensure that the code is reliable and bug-free, but even
Microsoft warrants only workmanship of the materials they distribute, not that
their software will do what they say it will do. Bill Gates has a lot more money
(and a lot more lawyers) than I
do, so I can only advise you to use this code at your own risk.
Holsinger, K. E., and R. J. Mason-Gamer. 1996. Hierarchical analysis of nucleotide diversity in geographically structured populations. Genetics 142:629-639.