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)