dna

POPDIST

Introduction

Documentation

Bugs and Comments

Getting the Program

Compiled Versions

UNIX

Macintosh

MS Windows

Program Source

References

New Versions

POPDIST

Introduction

popdist is a newly-developed population genetic data analysis program. popdist calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures.

popdist is special in that it includes a distance measure that works when comparing populations that are polyploid, and it even works when you compare populations that differ with respect to ploidy level. That means that you can estimate distances among your hexaploid populations and their distances to their diploid ancestors - and the differences will be on the same scale. This genetic distance also works for comparing parthenogenetic populations.

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.

At last...

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. popdist has two improvements. One is that due to a quirk of Cygwin the static linked Windows version required an extra dll - this has been worked around. Another is that you can now set screen width for the results output from the menu system.

Finally version 1.2.2 is here. It has internal improvements making popdist a little faster, more memory efficient and it has better support for Hedrick's genetic identity measure. Last but not least it has support for the Band Sharing Measure.

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.

Documentation

pdf 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".

Postscript The "computer note" is also available as postscript files. You can view postscript files on your computer using ghostview (under unix), ghostscript (for the macintosh) or GSview (under MS-Windows).

Example of a data file

There is an example data file available to demonstrate the input format. More examples are included with the distribution.

Bugs and Comments

If you discover any problem due to the program, however minor, we would like to hear about it. Please send e-mail to bernt.guldbrandtsen@agrsci.dk.

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.

Bugfixes

  • Version 1.0 had a serious problem. If you have downloaded that version please update to a later version.
  • Another small problem involves the program sometimes accepting to calculate identities for measures where these are not defined. Fixed.
  • Popdist got confused if the label for a population started with the letters 'pop'. Fixed.
  • There was a problem compiling on some types of unix, since I had changed the option letter for using the Nei (1978) measure to '-7' for consistency with the menus, but that wasn't allowed under aix, where option letters have to be letters (i.e. not numbers). Fixed.
  • UNIX versions of the program up to and including 1.0.3 have a problem in recognizing DOS style line endings. It's fixed in version 1.0.4.
  • When releasing version 1.1.0 I made a stupid mistake, which caused the output from the Cavallis-Sforza and Edwards measure to be wrong when using the jackknife procedure. It's fixed in version 1.1.1, which also fixes problems with the Cavallis-Sforza and Edwards measure on the mac.

Getting the program

POPDIST is available as either source code or as pre-compiled binaries.

Compiled Versions

Unix Versions

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.

Platform Operating System Download Version
SP2 AIX 4.2 Download 1.1.1
Intel Red Hat Fedora 14 (static, 64 bit) Download 1.2.4
Intel Red Hat Fedora 14 (static, 32 bit) Download 1.2.4
Silicon Graphics IP22 IRIX 6.5 Download 1.1.1
DEC alpha Digital UNIX v. 4.0D Download 1.1.1

How to...

Download the appropriate binary version - if available - and place it somewhere in a directory that is included in your $PATH.

CompressedAlternatively 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.

Macintosh

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.

Type Download Version
PowerMacintosh (any model) Download 1.1.1
68020 or better with FPU Download 1.1.1

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 :-).

Windows

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.

CompressedHere, you can download the source code as a zip file. or the binary below.

Platform Operating System Download Version
Intel Processors Windows Download 1.2.4
You also need a copy of the cygwin shared library. The library should be located in the same directory as the program file.

Source Code Archives

Compressed The complete source code of the program is available in various compressed formats.

Format Download
GNU zip popdist-1.2.4.tar.gz
Bzip2 popdist-1.2.4.tar.bz2
zip popdist-1.2.4.zip
xz popdist-1.2.4.tar.xz

New Versions and Other Good News

  • Version 1.0.1 fixes a problem with internal arrays for data being too small. I strongly urge you to upgrade to at least version 1.0.1.
  • Version 1.0.2 brings various small improvements. The menu system has been cleaned up. The help function has been improved and cleaned up. Also the command line option for choosing the measure of Nei(1978) has been renamed to -7 in order to be consistent with the menu.
  • The User's Guide for version 1.0.2 has also been expanded and corrected. Particularly the treatment of the menu system has been improved.
  • Version 1.0.3 fixes two small problems, one relating to a problem with the parsing of input files, when when individuals have a label staring with the letters 'pop', the other one was a small problem with some versions of the C-library, e.g. the one from AIX 4.2. The PC-executables are back.
  • Example data file This had been missing. There is now an example data file included in the source distribution. It is called example.dat
  • Version 1.0.4 Liselotte Wesley Andersen brought my attention to a problem affecting the use of the program under UNIX when working on a data file prepared under MS DOS. It has to do with the obnoxious differences in line endings. This problem is fixed in version 1.0.4.
  • Version 1.1.0 The measure of Cavalli-Sforza and Edwards (1967) has been added. There are also various minor improvements. I no longer have access to HP Unix and A/UX machines so these executables are gone. If you would like to obtain version 1.0.4 for either of those please email me.
  • Version 1.1.1 fixes two problems. The jackknife version of the Cavallis-Sforza & Edwards measure was broken, and the precompiled version for the mac was slightly broken.
  • Version 1.2.4 fixes a segmentation violation in the file parser.

References

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


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Bernt Guldbrandtsen
Dept. Molecular Biology and Genetics
Aarhus University
Box 50
DK-8830 Tjele
Denmark

Credits

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