fastlink README (version 3.0P)

From: ftp-bimas.dcrt.nih.gov
Last mod: June 11, 1997
allele | bugreport | checkpoint | constants | djgpp | install | ILINK | makefile | mapfun | memory | p4 | parallel | scaling | time | TreadMarks | trouble | unknown | updates |

portability : AIX | ALPHAVMS | DOS | IRIX | Linux | OSF | VAX | VMS |

extra PostScript documentations not part of the READMEs:

traverse.ps | loops.ps | unknown.ps

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.

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

A.A. Schaffer, Faster Linkage Analysis Computations for Pedigrees with
Loops or Unused Alleles, Human Heredity, to appear
This directory and its subdirectories contain version 3.0P 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 files paper1.ps and paper2.ps, and paper5.ps. Please cite the first two papers (so that all participants in the FASTLINK project get credit), 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 NIH, Rice University, and EBI. 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.

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

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@nchgr.nih.gov)


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