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)