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  estimates  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  maletheta  and  femaletheta are allowed to differ (sexdif is set to 1), then the number of dimensions
       doubles to 2 * (number of loci - 1). Estimating 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)