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*							      *
*                     TripleM version 1.0 		      *
*		        User's Manual			      *
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This software uses Partition Ligation strategy together with the EM 
algorithm to reconstruct haplotypes from unphased genotype data for 
nuclear family with single child. It also provides estimates on 
the population haplotype frequencies. The current version can be used on 
Linux and Windows platforms.

1. Installation on UNIX/LINUX

gunzip triplem.linux.gz 

2. Input Format

The user need to prepare an input file for the genotype data. The format is 
the same as in Pl-EM. That is, one line for each subject; in each line, each single nucleotide
polymorphism (SNP) occupies one space, no white space
is allowed between the neighboring loci. Each family is represented by three 
consecutive lines. The two parents followed by the child. there is no space between families or individuals.

For each SNP, by denoting "A" as the wild-type allele, and "a" as the
mutant allele. "?" denotes missing. The input formats for different genotype 
configurations are
illustrated below: 

	Heterozygous:				A/a --> 0
	Homozygous wild type:			A/A --> 1
	Homozygous mutant:			a/a --> 2
	missing: 				?/? --> 3

3. Command-line Arguments

The command for invoking the program is:

% plem input output top parSize bufSize round 

input  : the name of the file that contains the genotype information. 
	 Any name that is less than 20 characters in length would be
	 acceptable.
output : the name of the file that contains the haplotype information.
         Any name that is less than 20 characters in length would be
         acceptable. 
round  : the number of independent runs in each of the EM algorithm 
         implementation. This parameter has to be an integer, there is 
	 no limit for it and 20 is recommended. 
 
4. Program Output 

The output file is in plain text format that consists of two parts.

In the first part, for each subject in each family, the haplotype pairs predicted by the
software is listed, plus the ID number of each haplotype in the haplotype
pool of this population. 

The second part is the summary of the overall haplotype frequency and 
standard deviation for this population. All haplotypes that appeared in at 
least one of the subjects are listed. 

5. User Supports

All questions and comments should be directed to Steve Qin at the 
Department of Biostatistics, University of Michigan, Ann Arbor, MI 48105.
E-mail: qin@umich.edu