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)