'popmin'	calculation of minimal population sizes 
		in marker-assisted backcross programs

Usage:
  popmin [options] risk tmax d1 d2

parameters:
  d1, d2	distance (in Haldane CentiMorgans, double) from target
		gene to 'left' and 'right' markers, resp.; d1 must be 
		less than or equal to d2 (if not, interchange markers)
  tmax		maximal duration (in generations, integer)
		of backcross program
  risk		risk (double) of failure of backcross program
		(1-risk) = probability of at least one double recombinant
		in at most tmax BC generations

printing options:
  -h		print this help then exit
  -d		print 'detailed' results (default); 
		output complete information in a nicely readable fashion
  -a		print 'abbreviated' results;
		outputs only { n[t] (beta[t]) } for t in [1,tmax]
  -v		verbose mode, prints various intermediate results depending
		on optimization options
  -f <file>	results are put in file <file>; 
		otherwise to standard output (default)

breeding scheme options:
  -P<prob>	<prob> (double) is the probability of transmission of
		the target gene, see references for more details; default .5;
		note that prob<.5 implies different meaning for d1 and d2
  -I<index>	<index> of initial genotype (integer) to start recursion with;
		default is 3); possible genotypes at M1-T-M2 are:
			1) R-D-D ; 2) D-D-R ; 3) D-D-D 
		(with M1,M2: left and right markers ; T: target gene ;
		R: recipient type allele ; D: donor type allele)
  -i		same as above, except that genotype is entered
		interactively upon request

  With no breeding scheme option specified, default is '-P 0.5 -I 3'

population sizes options:
basic options:
  -t		tests particular population sizes n[t], to be entered
		interactively upon request; no optimization performed
		just computes probabilities of success for given n[t]
  -c		'constant'; minimal population sizes with n[t]=n for all t
  -s		'siman'; variable population sizes are computed using the 
		'simulated annealing' algorithm
  -e		'exhaustive'; variable population sizes are computed using an
		exhaustive search (could be very long)
additional options:
  -r		siman search expert option; seed for the ``Mersenne Twister''
		random number generator MT19937 used in 'siman' search
  -m		exhaustive search expert option; lower bound (integer) for
		search loops; default is 1
  -M		exhaustive search expert option; upper bound (integer) for
		search loops; default is defined by internal constant IMAX
  -p		exhaustive search expert option; step size (integer) for
		search loops; default is 1

  With no population size option specified, default is '-csd'


EXAMPLE:
  'popmin -cs .01 3 5.1 10.2'
	computes 'constant' and 'siman' minimal populations sizes over
	three backcross generations for flanking markers at 5.1 cM and 
	10.2 cM on each side of target gene, respectively, with an overall
	probability of success of .99 over the three generations

REFERENCES:
Hospital F. and Decoux G. (2001) popmin: a program for the numerical
	optimization of population sizes in marker-assisted backcross
	programs. J. Hered., submitted.
Hospital F. (2001) Lengths of intact chromosome segments surrounding
	introgressions and the reduction of linkage drag in marker-assisted
	backcross programs. Genetics, submitted.


Report bugs and comments to Frederic Hospital <fred@moulon.inra.fr>