Bugs and Comments
Getting the Program
This genetic distance measure that is being implemented here is the one developed by Jürgen Tomiuk and Volker Loeschcke. Tomiuk, Guldbrandtsen and Loeschcke (Genetica, 1998) have recently shown that in most cases this genetic distance measure has properties superior to other commonly used distance measures, and in particular it is more robust to deviations from the assumption of population genetic equilibrium.
Version 1.2.4 is here. This version fixes a bug in the file parser code. It caused a segmentation fault.
Version 1.2.3 is here.
Finally version 1.2.2 is here. It has internal
1.2.2 replaces version 1.2.1, which had a bug in the allele parser Thank you to Prijo Tanhuanpää for bringing this to my attention.
1.2.1 replaces version 1.2.0, which had a bug in the calculation of jackknife estimates. Thank you to Roland Vergilino for pointing this out.
A computer note has been published in The Journal of Heredity announcing the program. If you use the program please cite that note (See references). A draftcopy is available here. The user guide is also available. Note, that you need Adobe Acrobat Reader to read the user guide and the "computer note".
Example of a data file
There is an example data file available to demonstrate the input format. More examples are included with the distribution.
If you discover any problem due to the program, however minor, we would like to hear about it. Please send e-mail to email@example.com.
Also, if you succeed at compiling the program on platforms for which it is currently not available here on this web page, we would appreciate a copy, so that it can be made available on the net.
I am limited by the systems I have access to. If you succeed at compiling on other systems let me know or mail me the binaries, so that I can put them here.
Download the appropriate binary version - if available - and place
it somewhere in a directory that is included in your
Alternatively download the source code version. It is in the file popdist-1.2.3.tar.gz (compressed with GNU gzip), or in the file popdist-1.2.3.tar.bz2 (compressed with bzip2). Go to the directory where you saved the file. The following commands should then unpack and compile it assuming you downloaded the .gz version:
gunzip -c popdist-1.2.3.tar.gz | tar xovf - cd popdist-1.2.3 make popdist
The program is written in ANSI C, and should compile smoothly on ANSI C platforms. If it doesn't please, please send me an e-mail containing a description of the problem, version number of the program, platform you tried to compile on, what compiler you used, and other relevant information, so that I can fix.
Versions are available for both the Power Macintosh and for the older 680x0 models (that is before power). Both types are in MacBinary for safe transfer. Depending on your computers setup you may need a copy of StuffIt Expander or some other program that can convert MacBinary files back to proper Macintosh files. The Macintosh versions of the program are compiled with Metrowerks Codewarrior 4.
Since I don't know anything about mac programming the mac-interface is going to be goofy, i.e. as goofy as on the other platforms :-).
Binaries for Windows are available below. They are compiled using gcc from the wonderful Cygwin system. The executable requires the cygwin shared library, which is available below. The shared library is best located in the same directory as the popdist.exe executable. Alternatively you can install the whole Cygwin system by downloading and running the installer from Cygwin.
For the moment you will have to settle for the source code which ought to compile easily with any C or C++ compiler. If you have any problems using other compilers send me an e-mail.
Here, you can download the source code as a zip file. or the binary below.
The complete source code of the program is available in various compressed formats.
References about the Tomiuk & Loeschcke measure
Tomiuk, J. & Loeschcke, V. 1991, A new measure of genetic identity between populations of sexual and asexual species, Evolution, 45: 1685-1694.
Tomiuk, J. & Loeschcke, V. 1995, Genetic identity combining mutation and drift, Heredity, 74, 607-615.
Tomiuk, J. & Loeschcke, V. 1996, A maximum-likelihood estimator of the genetic identity between polyploid species, J. Theor. Biol., 179, 51-54.
Tomiuk, J., Guldbrandtsen, B., & Loeschcke, V. 1998, Population differentiation through mutation and drift - A comparison of genetic identity measures, Genetica, 102/103: 545-558.
Guldbrandtsen, B., Tomiuk, J., & Loeschcke, V. 2000, POPDIST, "Version 1.1.1: A Program to Calculate Population Genetic Distance and Identity Measures", The Journal of Heredity 91(2):178-179
Tomiuk, J., Guldbrandtsen, B. & Loeschcke, V. 2009, Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation, Mol. Ecol. Res. 9(5): 1364-1368
Other References of Interest
Cavalli-Sforza, L.L., & Edwards, A.W.F. 1967, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, 21: 550-570
Goldstein, D.B., Ruis Linares, A., Cavalli-Sforza, L.L., & Feldman, M.W. 1995, An evaluation of genetic distances for use with microsatellite loci, Genetics, 129: 463-471
Hedrick, P.W. 1971, A new approach to measuring genetic similarity, Evolution, 25: 276-280
Hillis, D.M. 1984, Misuse and modification of Nei's genetic distance, Syst. Zool., 33, 238-240
Nei, M. 1972, Genetic distance between populations, Amer. Natur., 106, 283-292
Nei, M. 1978, Estimation of average heterozygosity and geneitc distance from a small number of individuals, Genetics, 89: 583-590
Nei, M., Tajima, F., & Tateno, Y. 1983, Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data, J. Mol. Evol., 91: 153-170
Reynolds, J., Weir, B.S., & Cockerham, C.C. 1983, Estimation of the coancestry coefficient: Basis for a short-term genetic distance, Genetics, 105: 767-779
Rogers, J.S. 1972, Measures of genetic similarity and genetic distance, Studies in Genetics VII: 145-153, Univ. Texas Publ. 7213
Takezaki, N. & Nei, M. 1996, Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA, Genetics, 144: 389-399
You are number to access this page.Bernt Guldbrandtsen
Special thanks for helping me find bugs, making suggestions etc. (in order of appearance): Lars-Erik Holm, Liselotte Wesley Andersen.
Last modified: Tuesday Oct. 9, 2012