MQLS ("More Poweful" or "Modified" Quasi-likelihood Score Test).  A program for case-control association 
testing of a binary trait in samples that contain related individuals.  
Copyright(C) 2007 Timothy Thornton, Catherine Bourgain, and Mary Sara McPeek  
Homepage: http://galton.uchicago.edu/~mcpeek/software/MQLS

Release 1.1.  August 1, 2007
        1.2.  March 20, 2008
	1.3   February 23, 2009
        1.4   September 23, 2009
	1.5   March 14, 2011

Thanks to Daniel E. Weeks (weeks@pitt.edu) for improving the memory 
allocation and the handling of files with too many markers in Release 1.2.

Thanks to Mark Kvale (kvalem@humgen.ucsf.edu) for improving the memory          
allocation in Release 1.4.                  


The MQLS program can be considered as a significantly enhanced version
of the CC-QLS Program, copyright(C) 2003 Catherine Bourgain, Carole Ober, 
Mary Sara McPeek 
Homepage: http://galton.uchicago.edu/~mcpeek/software/CCQLSpackage1.3/index.html

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License

This program is free software; you can redistribute it and/or 
modify it under the terms of the GNU General Public License 
as published by the Free Software Foundation; either version 3 
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY of 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 (see file gpl.txt); if not, write to the 
Free Software Foundation, Inc., 59 Temple Place - Suite 330, 
Boston, MA 02111-1307, USA.

We request that use of this software be cited in publications as
Thornton T., McPeek M. S. (2007) "Case-Control Association Testing 
with Related Individuals: A More Powerful Quasi-Likelihood Score 
Test" American Journal of Human Genetics, vol 81, pp. 321-337.

To contact the first author:

Timothy A. Thornton, Ph.D.
Assistant Professor
Department of Biostatistics
University of Washington
Seattle, WA 98195-7232

email: tathornt@u.washington.edu



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Installation instructions:

1.  Download the MQLS package which includes the 'MQLS.c' program.
    
2.  Read the files 'MQLS_Overview', 'MQLS_Input', 'MQLS_Output' and 
    'MQLS_Tips' carefully to understand the purpose of this program and how 
    it works.
  
3.  Edit the 'Makefile' as necessary according to the instructions in
    the 'Makefile'.  You should only need to make sure that the correct
    compiler and compiler options for your machine are chosen.

4.  Type 'make'.  This will build an executable program 'MQLStest'.

5.  To run the executable program 'MQLStest':

    First, prepare the input files, e.g., 'markid', 'kinshipcoef', and 
    'prevalence' (see the file 'MQLS_input' for more details).

    Then,

      I.  to use option 1 (all individuals, affecteds, unaffecteds, and 
          individuals with unknown phenotype, are included in the 
          analysis), type

            ./MQLStest markid kinshipcoef prevalence 1

      II. to use option 2 (individuals with unknown phenotype are 
	  excluded from all tests, and individuals with missing 
          genotype data at a marker are excluded from the the test at
	  that marker), type

           ./MQLStest markid kinshipcoef prevalence 2

6.  Results of all genetic markers tested are output to a file called 'MQLStest.out'.
    The top 20 markers with the smallest p-values are output to a file called 'MQLStest.top.'
    The number of markers output to this file can be decreased or increased by the user by
    changing MAXTOP (currently set to 20) in the MQLS.c source file.  Warnings may also be
     printed to a file called 'MQLStest.err'.
  
7.  You can test the executable program 'MQLStest' using option 1 by running it 
    with two different sets of input files :
    (1) 'markid_Hutt', 'kinshipcoef_Hutt', 'prevalence_Hutt' corresponding to data from a single large
         inbred pedigree (2 markers)
    (2) 'markid_sib', 'kinshipcoef_sib', 'prevalence_sib' corresponding to data from independent outbred
         nuclear families
    You can then compare your output (using option 1) in the file 'MQLStest.out' with 
    the correct output in the sample output files 'Hutt_MQLStest.out' or 'Sib_MQLStest.out'

9.  The programs stop if any errors are detected in the format of the 
    input files.