TMARG v1.0 Beta


INTRODUCTION :  This program, TMARG, is an association mapping tool. 
		For testing statistical significance of phenotypes, TMARG uses
		both total phenotype likelihood (TPL) and maximum phenotype likelihood (MPL) 
		with haploid penetrance. TMARG takes a matrix of haplotypes or phase-known 
		genotypes and their phenotypes (i.e. case/control status) as input, and 
		provide point estimate for the complex trait loci.
		TMARG supports both a sampling of minARGs (ARGs using fewest number of 
                recombinations) in a sliding window, 
		and a faster (but more heuristic) ARG sampling for the entire data.
				
		TMARG reports strongest point estimate in the data, using both 
		total phenotype likelihood (TPL) and maximum phenotype likelihood (MPL).

                TMARG is tested on Linux machines, as well as Windows 
                (with cygwin).  

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SYNOPSIS: TMARG -Ck -Tk  [ -A ] data-filename

OPTIONS:
  -C		Specify the number of case haplotypes in the data. Note that
		the case haplotypes should appear first in the data. 

  -T		Specify the number of samples to draw from the space of
		all possible genealogies. It might be good to start
		from k=50.

  -A		Activate the slower (but converge better) sampling of sliding window. 
                By default (i.e. if -A not specified),
		TMARG constructs ARGs for the entire data.

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DATA FILE    :  The first line of the data file is IGNORED.  If you like,
                you may put a description of the data there.
                The data should be in 0,1. (White space is allowed 
                between columns.)  Each sequence should be placed in a its
                own row. No SPACE between two values, please. 

		Also, you should group the case haplotypes and control haplotypes
		seperately, with cases showing up first.

                Note that it is often desirable to specify physical distance of SNPs.
                You can enter a list of positions (in integers) as the FIRST line of data.
                Thes physical distance will be read by TMARG and then used to report
                strongest association locus.

EXAMPLE      :  An example data set (simple-example.dat) is included.
                Try running "./TMARG -C1 Kreitman.dat" to 
                check that everything works correctly.
		   
CONTACT      :  Please send bug reportss and technical questions to Yufeng Wu at 
                <wuyu@cs.ucdavis.edu>.