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


       ilink [options] ipedfile.dat pedfile.dat


       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


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


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



       Alejandro Schaeffer <> and others

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

                                April 15, 2003