From: softlib.cs.rice.edu                       Last mod: March 5, 1995

                  FASTLINK, version 2.2

Each section in each README file starts with the string "|*|". To
browse the sections, use your file viewer to search for this unique
string. This is the top level README file.


|*| INTRODUCTION
    ------------

As described in the papers:

R. W. Cottingham Jr., R. M. Idury, and A. A. Schaffer, Faster Sequential 
Genetic Linkage Computations, American Journal of Human Genetics, 53(1993),
pp. 252-263.

and

A. A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham, Jr.,
Avoiding Recomputation in Genetic Linkage Analysis, Human Heredity,
44(1994), pp. 225-237.

this directory and its subdirectories contain version 2.2 of faster
versions of the general pedigree programs of LINKAGE 5.1.
Several of our users of earlier versions 1.0 and 1.1 have dubbed the new
programs FASTLINK.  A PostScript version of the papers can be found in
the file paper1.ps and paper2.ps.  Please cite both papers if you use
these programs in a published experiment. You should continue to cite
the original papers on LINKAGE, listed below, if you use FASTLINK:

G. M. Lathrop, J.-M. Lalouel, C. Julier, and J. Ott, Strategies for
Multilocus Analysis in Humans, PNAS 81(1984), pp. 3443-3446.

G. M. Lathrop and J.-M. Lalouel, Easy Calculations of LOD Scores
and Genetic Risks on Small Computers, American Journal of Human Genetics,
36(1984), pp. 460-465.

G. M. Lathrop, J.-M. Lalouel, and R. L. White, Construction of Human
Genetic Linkage Maps: Likelihood Calculations for Multilocus Analysis,
Genetic Epidemiology 3(1986), pp. 39-52.


The FASTLINK code is available by anonymous ftp to a machine at Rice
University.  For instructions see the file README.install.

In addition to the two papers and this README file, the top level
directory contains various other pieces of documentation. Carol Haynes
(Duke) suggested that we split up the documentation into smaller
pieces. This file is primarily a roadmap to the documentation for FASTLINK.

README.bugreport  --- suggest how to send in a bug report

  |*| How to Submit a Useful Bug report

README.checkpoint --- explains the checkpointing scheme for LODSCORE and
                      ILINK
  |*| Introduction to checkpointing
  |*| The Process
  |*| The Files
  |*| Modifying Scripts and Checkpointing
  |*| Using the Script-Level Checkpointing Facility
  |*| Important Caution on Breaking a ckpt Run

README.constants --- explains the mysteries of how to properly set some
                     of the constants in FASTLINK
  |*| Constant Definitions - VERY IMPORTANT!!
  |*| Setting Constants by Editting only the Makefile

README.djgpp --- explains how to retrieve and install the djgpp C compiler
                 for those who want source code for FASTLINK for DOS.
                 The compiler is free.

  |*| Introduction
  |*| File Retrieval
  |*| Installing djgpp and compiling FASTLINK

README.ILINK --- What does the output of ILINK and LODSCORE mean?

README.install -- explains basic facts about retrieving and installing FASTLINK
  |*| FTP Directions
  |*| Source Code Organization
  |*| Compilation

README.memory  --- explains memory requirements
  |*| Memory Requirements

README.portability --- contains summary of portability information
                       and refers to the following files for more
                       information regarding specific operating systems
                       Note: README.portability and the following
                       system-specific files are not included in the
                       diskette version of FASTLINK for DOS.

  README.AIX
  README.ALPHAVMS
  README.DOS
  README.IRIX
  README.Linux
  README.OSF
  README.VAX
   |*| Instructions for DEC C Compiler
   |*| Instructions for VAX C Compiler
  README.VMS

README.scaling --- LINKMAP users should read this file
  |*| Scaling Alert for LINKMAP users

README.updates --- explains noticeable changes in different versions of
                   FASTLINK
  |*| Changes Introduced in version 1.1
  |*| Changes Introduced in version 2.0
  |*| Changes Introduced in version 2.1 and while maintaining 2.0
  |*| Changes Introduced in version 2.2 and while maintaining 2.1

The following are PostScript files (traverse.ps takes a while to print)
They are not included in the diskette version of FASTLINK for DOS.

traverse.ps --- explains the pedigree traversal algorithm in great detail
                with examples
loops.ps --- explains various aspects of loops in LINKAGE/FASTLINK.

unknown.ps --- explains how the UNKNOWN preprocessor program works.

Send suggestions for other FASTLINK documentation you would like to see to
schaffer@cs.rice.edu.

We are working on further sequential improvements, and parallel
implementations of the code. These will be integrated over time.

Please let us know if you have problems with the programs,
including if you are unhappy with the speedup and are willing to
share your data to the extent that we may be able to study the
problem. Note that this does not mean you have to tell us
anything about what disease you are studying. And of course we
will respect any request for confidentiality. We only wish to
consider studying problems to see if we can find improvements.

If you read README.updates you will see that lots of the updates are
suggested by users who are enthusiastic about FASTLINK, but would
like to see it improve. One of the best ways to encourage us to
work harder on FASTLINK is to send in your constructive suggestions.

Also please tell us if your experience is positive. (send email to
Alejandro Schaffer at schaffer@cs.rice.edu)