---------------------------------------------------------------------- DDDD ff ff IIIII D D f f I t D D ii fff fff eee rrr I nnn ttt D D i f f eee r I n n t DDDD iii f f eee r IIIII n n t (November 2014) ---------------------------------------------------------------------- DifferInt: Compositional differentiation among populations at three levels of genetic integration Copyright (C) 2008-2014 Elizabeth M. Gillet (excepting implemented open source code RELAX-IV of Bertsekas & Tseng: http://elib.zib.de/pub/Packages/mathprog/mincost) DifferInt is free software: you can redistribute it under the terms of the GNU General Public License (GPL) v.3, as published by the Free Software Foundation. DifferInt is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see www.gnu.org/licenses. ---------------------------------------------------------------------- Download at http://www.uni-goettingen.de/forstgenetik/differint or http://projects.gwdg.de/projects/differint ---------------------------------------------------------------------- DifferInt calculates compositional differentiation among populations of diploid individuals for codominant markers at three levels of genic integration[1]: Gene pool, single-locus genotypes, multilocus genotypes Measures considering elementary genic difference between genetic types Pairwise distance "Delta" between populations[3,4] Complementary differentiation "Delta_SD" among populations[1,2] Dispersive differentiation "Delta-bar" among populations[1] Measures neglecting elementary genic difference between genetic types Pairwise distance "d_0" between populations[5-7] Complementary differentiation "delta_SD" among populations[1,8] Dispersive differentiation "delta-bar" among populations[1] Permutation analyses: Effect of gene association within populations[1] Covariation of pop.contributions between integration levels[1] Effect of genes and their associations among populations[1,2] References: [1] Gillet EM (2013) DifferInt: Compositional differentiation among populations at three levels of genetic integration. Molecular Ecology Resources 13, 953-964. http://dx.doi.org/10.1111/1755-0998.12145 [2] Gillet EM, Gregorius H-R (2008) Measuring differentiation among populations at different levels of genetic integration. BMC Genetics 9, 60. http://dx.doi.org/10.1186/1471-2156-9-60 [3] Gregorius H-R, Gillet EM, Ziehe M (2003) Measuring differences of trait distributions between populations. Biometrical Journal 45(8), 959-973. [4] Gillet EM, Gregorius H-R, Ziehe M (2004) May inclusion of trait differences in genetic cluster analysis alter our views? Forest Ecology & Management 197, 149-158. [5] Gregorius H-R (1974) On the concept of genetic distance between populations based on gene frequencies. Proceedings, Joint IUFRO Meeting S.02-04, 17-22. [6] Gregorius, H.-R. (1987) The relationship between the concepts of genetic diversity and differentiation. Theoretical & Applied Genetics 74, 397-401. [7] Gregorius H-R (1984) A unique genetic distance. Biometrical Journal 26, 13-18. [8] Gregorius H-R, Roberds JH (1986) Measurement of genetical differentiation among subpopulations. Theoretical and Applied Genetics 71, 826-834. ---------------------------------------------------------------------- INSTALLATION AND EXECUTION OF THE PROGRAM -------- Windows: Compiled with GNU FORTRAN (mingw32) under Win XP -------- Download from http://www.uni-goettingen.de/forstgenetik/differint or http://projects.gwdg.de/projects/differint Move to the directory in which you want it to run. Change to this directory. Unzip . A directory is created named . Open directory Contents of directory DifferInt.exe [executable] DifferInt-Manual.pdf [manual] exa1.txt [example input file] exa2.txt [example input file] metapop1.dat [example input file] metapop2.dat [example input file] metapop3.dat [example input file] metapop4.dat [example input file] Gillet-Gregorius-BMCGenetics-2008.pdf [original publication] GNU-General-Public-License.txt [license for use] README [this file] Start An interactive window calls for an input file such as the example input and . See for input specifications. Select options as described in . If no selections are made, the program runs with defaults. ------ Linux: Compiled with GNU FORTRAN under opensuse12.2 ------ Download from http://www.uni-goettingen.de/forstgenetik/differint or http://projects.gwdg.de/projects/differint Move file to the directory where you want it to run: > mv DifferInt-linux.tar Mydirectory Change to this directory > cd Mydirectory Unpack using > tar -xvf DifferInt-linux.tar Open directory > cd DifferInt-linux Contents of directory >ls DifferInt [executable] DifferInt-Manual.pdf [manual] exa1.txt [example input file] exa2.txt [example input file] metapop1.dat [example input file] metapop2.dat [example input file] metapop3.dat [example input file] metapop4.dat [example input file] Gillet-Gregorius-BMCGenetics-2008.pdf [original publication] GNU-General-Public-License.txt [license for use] README [this file] Start execution > ./DifferInt An interactive window calls for an input file such as the example input and . See for input specifications. Select options as described in . If no selections are made, the program runs with defaults. !!!!!!!! IMPORTANT NOTE FOR LINUX USERS !!!!!!!!!! from Helmut Michels : On some computers, warnings of the following type appear Warning: translation table syntax error: Unknown keysym name: osfActivate Warning: ... found while parsing ':osfActivate: ManagerParentActivate()' As explained by Helmut Michels in the DISLIN Discussion Group, when a program that uses DISLIN widgets is executed on a recent or older Linux system than the one on which it was created, warnings of this type may appear. The reason is that the location of the file XKeysymDB used by the widgets can differ between Linux systems. A workaround is to define the environment variable XKEYSYMDB with the location of the XKeysymDB file. Thus if > find /usr/ -name XKeysymDB or > locate XKeysymDB returns location, then enter > export XKEYSYMDB=location For example, if location is /usr/share/X11/XKeysymDB, then type > export XKEYSYMDB=/usr/share/X11/XKeysymDB and restart the program by typing > ./DifferInt Send comments, suggestions, and bug reports to differint@uni-goettingen.de. ---------------------------------------------------------------------- Changes made in earlier versions ---------------------------------------------------------------------- Since version of June 2014: - Corrected made to maximum number of allele "names" that led to an error when the total number of allele names was larger than the total number of individuals - Improved formatting in several output files Since version of April 2014: - A formatting error in the output files d0matrix.txt and Deltamatrix.txt has been corrected that caused entries in longer rows of the matrix to be printed one per line. - Interactive and console-based input now offers three different ways to submit the list of loci for which calculations are to be performed: "All loci", a short list of loci typed into the console, and specification of a text file from which the list of loci is to be read. - A formatting error has been corrected that terminated the listing of loci at 60 in the output window when calculations were performed for more loci. Since version of June 2013: - Improved formatting in the files .d0matrix.txt and .Deltamatrix.txt, .alleles.txt, .snglgeno.txt, and .multigeno.txt