                  Welcome to GENEHUNTER

* What is GENEHUNTER

GENEHUNTER is a software package that allows the very rapid extraction
of complete multipoint inheritance information from pedigrees of
moderate size.  This information is then used in exact computation of
multipoint LOD scores and in a powerful new method of non-parametric
linkage analysis.  Quick calculations involving dozens of markers,
even in pedigrees with inbreeding and marriage loops, is possible with
GENEHUNTER.  In addition, the multipoint inheritance information
allows the reconstruction of maximum-likelihood haplotypes for all
individuals in the pedigree and information content mapping which
measures the fraction of the total inheritance information extracted
from the marker data.  All of these calculations are performed in a
user-friendly environment familiar to MAPMAKER, SIBS, or HOMOZ users.


* How to Obtain GENEHUNTER

The first step is to obtain the file gh-1.3.tar.gz from our network site
genome.wi.mit.edu in the distribution/software/genehunter subdirectory.
This can be done via ftp or any number of network tools.  Login with
the username anonymous and then enter your e-mail address as a password.

======================================================================
Registered users (see form at bottom) will receive notification of
any new versions.
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* How to Install GENEHUNTER

To extract the GENEHUNTER files from this file, create a subdirectory 
for the program, move the gh-1.3.tar.Z file into it, and enter the commands:

     gunzip gh-1.3.tar.gz
     tar xvpf gh-1.3.tar

The directory will now be filled with the following files:

gh.sun         - the GENEHUNTER executable for Sun Sparcstations
gh.alf         - the GENEHUNTER executable for DEC Alpha machines
gh.help        - on-line help file - do not edit!
gh.ps          - PostScript version of on-line help for printing
Makefile       - Unix Makefile for compilation on other systems
linkloci.dat   - sample marker data file
linkped.pre    - sample pedigree data file
xgh.sun        - the GENEHUNTER X chromosome executable for Sun Sparcstations
xgh.alf        - the GENEHUNTER X chromosome executable for DEC Alpha machines
xgen.loc       - sample X chromosome marker data file
xgen.ped       - sample X chromosome pedigree data file

along with the subdirectories src and ansilib which contain the source code
for the program.  If the extraction is successful, you can now delete the
gh.tar archive.


* Compiling GENEHUNTER

If you are planning to run GENEHUNTER on a Sun Sparcstation running
SUNOS or a DEC Alpha running OSF, you can use the precompiled
executables "gh.sun" or "gh.alf".  If you have another type of
Unix machine, you must compile the code yourself to create an
appropriate executable version.  One or two simple changes must be
made to the Makefile:

1) line 5 (SYS= -D_SYS_SUNOS) must be replaced with one of the following:

	SYS= -D_SYS_SUNOS   - for compilation on SUN machines
	SYS= -D_SYS_OSF     - for compilation on DEC/Alpha machines
	SYS= -D_SYS_ULTRIX  - for compilation on Ultrix systems
	SYS= -D_SYS_HPUX    - for compilation on HP workstations
	SYS= -D_SYS_AIX     - for compilation on IBM/AIX RISC systems
	SYS= -D_SYS_SOLARIS - for compilation on Solaris machines

   (If your system is not listed among those above, you can probably use one
    of the above definitions anyway - for example -D_SYS_OSF adheres to the
    ANSI standard and can be used with almost any ANSI compiler)

2) line 12 in Makefile (CC = gcc) determines the C-compiler to be called
   and should be replaced if another C-compiler is used on your system
   (for example, CC = cc)

After the Makefile is edited for your system, the Unix command "make"
should automatically create the executable "gh" appropriate for
your system.  If compilation is unsuccessful, contact your system
administrator for assistance first as he or she will be familiar with
bringing code to your particular system.  If further assistance is
required, feel free to contact us for help.


* Getting Ready to Run

It will often be useful to store your data in a separate subdirectory
from the GENEHUNTER program (for various reasons such as diskspace or
to make the program available to multiple users).  In such cases, it
can be helpful to include the directory containing the GENEHUNTER
program in your Unix path. In addition, to use the on-line help
facility, you will need to inform the program where to find the help
and related documents.  For instance, if the subdirectory you created
for the programs is named /home/GH, you will want to change your
.cshrc file as follows:

1. change the line which reads something like:

     set path=(. /bin /usr/local /usr/bin /etc) 

   to include /home/GH

     set path=(. /bin /usr/local /usr/bin /etc /home/GH)

2. add the following line to the end of the file

     setenv GH_DIR /home/GH

Now GENEHUNTER can be called from anywhere on your system by simply
typing the executable name (gh or gh.sun).

(If you wish to hardwire the GH_DIR into the code, replace the body
of get_code_directory in ansilib/syscode.c with the line:
nstrcpy(buf,<your GH directory>,PATH_LENGTH); return(TRUE);
and recompile.)

* Using GENEHUNTER

To run the program just type the name of the executable and
the shell will start up.  To get a quick start in running the commands
enter 'help basic' at the prompt.

* How to cite or get more information on GENEHUNTER 

L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. "Parametric and
Nonparametric Linkage Analysis: A Unified Multipoint Approach". 
American Journal of Human Genetics 58:1347-1363 (June 1996).

L. Kruglyak and E.S. Lander. "Faster Multipoint Linkage Analysis
Using Fourier Transforms". Journal of Computational Biology 5:1-7 (1998).


* Reporting Bugs or Errors:

Please contact us with any bugs or difficulties you may discover while
running this program and we will do our best to help you out.  If you are
having difficulty installing or obtaining the program, ask your resident
system manager for help as he or she will be more familiar with the
commands appropriate for your system.  E-mail is the best way to contact
us regarding questions or problems with the program itself:

     leonid@genome.wi.mit.edu
     mjdaly@genome.wi.mit.edu

* License Agreement

Copyright (c) 1995
        Whitehead Institute for Biomedical Research. All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1.      Redistributions must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the  documentation
and/or other materials provided with the distribution.  Redistributions of
source code must also reproduce this information in the source code itself.

2.      If the program is modified, redistributions must include a notice
(in the same places as above) indicating that the redistributed program is
not identical to the version distributed by Whitehead Institute.

3.      All advertising materials mentioning features or use of this
software  must display the following acknowledgement:
        This product includes software developed by the
        Whitehead Institute for Biomedical Research.

4.      The name of the Whitehead Institute may not be used to endorse or
promote products derived from this software  without specific prior written
permission.

We request that users of this software inform us by sending email to
software_registration@genome.wi.mit.edu.

We also request that use of this software be cited in publications as:
L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. "Parametric
and Nonparametric Linkage Analysis: A Unified Multipoint Approach".
American Journal of Human Genetics 58:1347-1363 (June 1996).  For
versions 1.2 and above, please also cite: L. Kruglyak and
E.S. Lander. "Faster Multipoint Linkage Analysis Using Fourier
Transforms".  Journal of Computational Biology 5:1-7 (1998).

THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND  ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  ARE
DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE  FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL  DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)  HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.

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SOFTWARE USAGE E-MAIL NOTIFICATION FORM

We appreciate your interest in the software developed at the MIT Genome
Center, and we would be grateful if you could drop us a note telling us
that you are using it (among other things, this information is very helpful
to us when preparing our grant renewal applications!).  Could you please
take a moment to fill out this form and mail it to
software_registration@genome.wi.mit.edu?

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