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DDDD   EEEEE  L   TTTTT   AAA   SSSSS
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DDDD   EEEEE  LLLL  T    A   A  SSSSS   version 2.0 for Linux, 2008
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<DeltaS> calculates the measure of pairwise distance "Delta" between
populations, which takes into account the frequencies of the trait states
(types) and the pairwise differences between the types. For each pair of
populations, "Delta" expresses the minimum degree to which the frequency
distribution of the types within one population must be transformed in order
to make it match the distribution in the other population ([2], [5]). "Delta"
reduces to the absolute genetic distance "d_0" ([3], [4]), if differences
between types are equal to 1.


INPUT TO <DeltaS>:

* Information requested by query:

  o Number of POPULATIONS (integer)
  o Number of TYPES (integer)
  o FORM of input of TRAIT DIFFERENCES d(i,j) between types i and j: "U" for
    UPPER DIAGONAL differences (i>j) or "L" for LOWER DIAGONAL differences
    (i<j) (default="L") 
  o TRAIT DIFFERENCES d(i,j) between types
  o Maximum NUMBER of matrix COLUMNS per line of output at 8 characters per
    column + 9 leading characters: Larger matrices are printed blockwise
    (default="8" columns per line) 
  o Show OPTIMAL TRANSFORMATIONS in output? "Y"=yes (default="N")
  o FREQUENCIES of the TYPES in the POPULATIONS: All integer and decimal
    entries are normalized through division by their population sum. 

* For queries that request more than one number, the numbers can be separated
  by commas, blanks, tabs, or carriage returns ("Return"). 

* The input can be entered in two ways:

  o Start <DeltaS>, which opens a console window, and type in the answers to
    the queries. 
  o Prepare an input file with a text editor in advance, for example as a file
    named "input.txt", in the <DeltaS> directory. Run <DeltaS> by opening a
    console window (e.g. MS-DOS window, xterm in Linux), change the directory
    to the <DeltaS> directory, and type in the command 
            "DeltaS.exe  <  input.txt"  (for W32)  
         or "./Delta < input.txt"       (for Linux) 


OUTPUT FROM <DeltaS>:

Besides being printed to the console window, the output is printed to the
following files: 

* "outsummary.txt" and screen:  Summary of results, comprising

  o Trait differences between types
  o Frequencies of the types in the populations
  o Optimal transformations, if selected
  o Pairwise distances "Delta" between populations
  o Pairwise distances "d_0" between populations

* "outdelta.txt":  Pairwise distances Delta between populations (input for
   other programs) 

* "outd0.txt":  Pairwise distances "d_0" between populations (input for other
   programs) 


PROGRAM NOTES:

* <DeltaS> is compiled using the GNU Fortran compiler g77 for Windows (32-bit
  Win98 and WinXP) and the GNU Fortran compiler gfortran for Linux 
  (SuSE 10.3).  
* The minimum degree of transformation is a solution of the Transportation
  Problem, for which <DeltaS> incorporates open source code from the program
  RELAX-IV [1]. 
* Send comments, suggestions, and bug reports to <egillet@gwdg.de>



DOWNLOAD FROM URL http://www.uni-forst.gwdg.de/forst/fg/software/deltas.htm

deltas-2.0-W32.zip - <DeltaS> for Win32 - 
Contents:
    * DeltaS.exe
    * README
    * COPYING

deltas-2.0-linux.tar.gz - <DeltaS> for Linux - 
Contents:
    * DeltaS
    * README
    * COPYING


REFERENCES:

[1] Bertsekas D.P., Tseng P. 1994. RELAX-IV: A faster version of the RELAX
    code for solving minimum cost flow problems.
    http://elib.zib.de/pub/Packages/mathprog/mincost/relax-4/

[2] Gillet E.M., Gregorius H.-R., Ziehe M. 2003. May inclusion of trait
    differences in genetic cluster analysis alter our views? Forest Ecology
    and Management 197, 149-158,
    2004. http://dx.doi.org/10.1016/j.foreco.2004.05.010

[3] Gregorius H.-R. 1974. Genetischer Abstand zwischen Populationen. I. Zur
    Konzeption der genetischen Abstandsmessung. Silvae Genetica 23: 22-27.
    http://www.bfafh.de/inst2/sg-pdf/23_1-3_22.pdf

[4] Gregorius H.-R. 1984. A unique genetic distance. Biometrical Journal
    26:13-18. http://dx.doi.org/10.1002/bimj.4710260103

[5] Gregorius H.-R., Gillet E.M., Ziehe M. 2003. Measuring differences of
    trait distributions between populations. Biometrical Journal 45:
    959-973. http://dx.doi.org/10.1002/bimj.200390063


<DeltaS> Copyright  2003-2008 Elizabeth M. Gillet 
(excepting code of RELAX-IV [1]).  
Email egillet@gwdg.de
URL http://www.uni-forst.gwdg.de/forst/fg/software/deltas.htm

<DeltaS> 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. <DeltaS> 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. Reassembling is not permitted. For details
see the GNU General Public License, a copy of which is contained in the file
COPYING included in the download file, or see http://www.gnu.org/licenses/.

CONTACT:

Elizabeth M. Gillet    +49-551-393535    egillet@gwdg.de
