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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         (October 2016)     
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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 <DifferInt-W32.zip>
from http://www.uni-goettingen.de/forstgenetik/differint 
or   http://projects.gwdg.de/projects/differint

Move <DifferInt-W32.zip> to the directory in which you want it to run.

Change to this directory.

Unzip <DifferInt-W32.zip>. A directory is created named
<DifferInt-W32>.

Open directory <DifferInt-W32>

Contents of directory <DifferInt-W32>
   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 <DifferInt.exe>

An interactive window calls for an input file such as the example
input <exa1.txt> and <exa2.txt>. See <DifferInt-Manual.pdf> for input
specifications.

Select options as described in <DifferInt-Manual.pdf>.  If no
selections are made, the program runs with defaults.


------
Linux: Compiled with GNU FORTRAN under opensuse12.2
------

Download <DifferInt-linux.tar>
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 <DifferInt-linux>
> cd DifferInt-linux

Contents of directory <DifferInt-linux>
>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 <exa1.txt> and <exa2.txt>. See <DifferInt-Manual.pdf> for input
specifications.

Select options as described in <DifferInt-Manual.pdf>.  If no
selections are made, the program runs with defaults.


!!!!!!!! IMPORTANT NOTE FOR LINUX USERS !!!!!!!!!!
from Helmut Michels <http://www.dislin.de>: 

On some computers, warnings of the following type appear

Warning: translation table syntax error: Unknown keysym name: osfActivate
Warning: ... found while parsing ':<Key>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 <prefix>d0matrix.txt and
  <prefix>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 <prefix>.d0matrix.txt and
  <prefix>.Deltamatrix.txt, <prefix>.alleles.txt,
  <prefix>.snglgeno.txt, and <prefix>.multigeno.txt


Since version of November 2014:

- Fixed bug for calculation of unequal population sizes. 

- Changed extension of filenames containing input for snails plots 
  from .in to .txt

- Adjusted formatting of output files
