ilink(1) [linux man page]

ILINK(1)						      General Commands Manual							  ILINK(1)

NAME

       ilink - GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions

SYNOPSIS

       ilink [options] ipedfile.dat pedfile.dat

DESCRIPTION

       This  manual page documents briefly the ilink command.  In fact this is a very raw intend to provide a manpage because the Debian GNU/Linux
       distribution requires each program to have a manpage.  Any enhancement would be greatly apreciated.

       ilink is part of the fastlink software package.

       ILINK uses the GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions. If you use the
       default	scripts  produced  by  lcp, your initial guess for theta is .1 in every dimension.  GEMINI evaluates each theta by its likelihood,
       seeking to find theta vectors that have a higher pedigree likelihood.

       The GEMINI procedure has multiple iterations. Each iteration corresponds to one line of output. Each iteration includes multiple likelihood
       function  evaluations.  Each iteration has two phases. In Phase I GEMINI seeks to improve the current best theta. In Phase II, GEMINI esti-
       mates the gradient of the likelihood with respect to the current best theta vector. In the first iteration,  Phase  I  only  evaluates  the
       likelihood at the initial candidate theta.

       When  ILINK  prints  out  a line such as: maxcensor can be reduced to -32767, it has completed the first likelihood function evaluation. On
       long runs, this fact can be used to estimate running time. A reasonable rough estimate for the number of function evaluations is 10*(number
       of  dimensions  of theta vector). The number of dimensions of the theta vector is one fewer than the number of loci in most cases. If male-
       theta and femaletheta are allowed to differ (sexdif is set to 1), then the number of dimensions doubles to 2 * (number of loci - 1).  Esti-
       mating other parameters (with fitmodel set to true) can also increase the number of dimensions.

       To learn more about ilink it might be useful to read the file /usr/share/doc/fastlink/README.ILINK if you have a Debian GNU/Linux system.

OPTIONS

       There might be options but I did not found any information about them.  Please foreward any information about them to <tille@debian.org>

SEE ALSO

       linkmap(1), lodscore(1), mlink(1), unknown(1).

Word-Wide-Web:
       http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html

AUTHOR
:
       Alejandro Schaeffer <schaffer@helix.nih.gov> and others

       This manual page was written by Andreas Tille <tille@debian.org>, for the Debian GNU/Linux system (but may be used by others).

								  April 15, 2003							  ILINK(1)

DSDP(1) 						      General Commands Manual							   DSDP(1)

NAME

       dsdp5 - semidefinite program solver

SYNOPSIS

       dsdp5 [options] filename
       maxcut [options] filename
       theta  filename

DESCRIPTION

       This manual page documents briefly the dsdp5, theta and maxcut commands.

       dsdp5 -- interface to solve general semi-definite programs
       maxcut -- solves a SDP relaxation of the maximum cut problem
       theta -- solves the Lovasz thetha problem

OPTIONS

       A summary of options is included below.	For a complete description, see /usr/share/doc/dsdp-doc.

       -help  Show summary of options.

       -v, --version
	      Show version of program.

       -print print information at each k iteration (default 10)

       -save  filename of solution file in SDPA format

       -fout  filename to print standard monitor to a file

       -y0    filename for initial solution file

       -benchmark
	      filename to file containing names of SDPA files

       -directory
	      path to directory containing benchmark SDPA files

       -suffix
	      suffix to add to each benchmark problem name

       -dloginfo
	      print more information for higher numbers (default 0)

       -dlogsummary
	      print timing information (default 1 - enabled)

       -gaptol
	      gap tolerance parameter, stop when relative duality gap less than this gap (default 1e-6)

       -r0    if nonnegative, initialize S by adding this multiple of the identity matrix (default -1)

       -penalty
	      penalize dual infeasibility (default 1e10)

       -boundy
	      bound for variables y (default 1e7)

       -maxit set maximum iterates (default 200)

       -zbar  Upper bound for dual solution (default 1e10)

       -mu0   if positive, set initial barrier parameter (default -1)

       -rho   Potential parameter as multiple of dimension (default 3)

       -drho  Use dynamic rho strategy (default 1)

       -pnormtol
	      stop only if pnorm less than (default 1e30)

       -reuse Reuse the Schur Matrix this many times (default 4)

       -dobjmin
	      apply a known lower bound for the objective at solution as a constraint.

       -bigM  if positive, modify algorithm to make dual infeasibility positive with a large associated cost (default 0)

       -dloginfo
	      print more information for higher numbers  (default 0)

       -params
	      filename to read selected options from a file

SEE ALSO

       glpsol(1),

       The programs are documented fully in the accompanying .pdf and html documentation
	      which can be found in /usr/share/doc/dsdp-doc if the dsdp-doc package is installed.

AUTHOR

       dsdp was written by Steven J. Benson <benson@mcs.anl.gov> and Yinyu Ye <yinyu-ye@stanford.edu>

       This manual page was written by Soeren Sonnenburg <sonne@debian.org>, for the Debian project (but may be used by others).

								  August  1, 2007							   DSDP(1)