FASTLINK 3.0P available

Alex Schaffer schaffer at cs.rice.edu
Mon Feb 5 17:26:02 EST 1996


I am pleased to announce that FASTLINK 3.0P is now available.
FASTLINK is an improved version of the linkage analysis package
LINKAGE 5.1, which is 
    --faster sequentially than LINKAGE, 
    --runs well in parallel, 
    --is more robust against errors, and 
    --includes substantial new documentation

The initial improvements that led to FASTLINK 1.0 are described in:

1. 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. (available as paper1.ps in the distribution)

The improvements that led to FASTLINK 2.0 are described in:

2. 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. (available as paper2.ps in the distribution)

The improvements that led to FASTLINK 3.0 are described in:

3. A. A. Schaffer, Faster Linkage Analysis Computations for Pedigrees
with Loops or Unused Alleles, Human Heredity, to appear. (available
as paper5.ps in the distribution)

We ask that you cite papers 1 and 2, as well as at least one paper
about LINKAGE, if you use FASTLINK in a published experiment.

paper3.ps and paper4.ps in the distribution describe how FASTLINK runs
in parallel.

As with previous versions, the code is available by ftp from:
   softlib.cs.rice.edu 

Login as anonymous, leave full e-mail address as password.  
   cd pub/fastlink

If you are a UNIX user:
   get fastlink.tar.Z

If you are a DOS user:
   cd dos
   <retrieve everything in that directory>

If you are a VMS user:
   get README
   get README.VMS
and follow the instructions there for what you need

Retrievers in Europe may find it more convenient to retrieve from the
mirror site at:
   ftp.ebi.ac.uk

The instructions are similar, but instead of:
   cd pub/fastlink   (for softlib)
do
   cd pub/software/linkage_and_mapping/FASTLINK/fastlink  (for ebi)

It takes up to 24 hours for the contents of the Rice site to get updated
at the U.K. mirror site.

Among the improvements in FASTLINK 3.0P (compared to 2.3P) are:

   -- The code runs faster on data sets that have loops or unused alleles
      If you used FASTLINK 2.3P, you may have noticed that it printed
      diagnostics when a data set had unused alleles, but it did not take
      advantage of the situation.

   -- UNKNOWN now detects violations of Mendelian rules of inheritance
      in looped pedigrees. It never did this before.

   
   -- maxhap and maxfem are no longer in the code as constants, except in
      UNKNOWN. If you were resetting maxhap each time and recompiling, you
      won't have to do that any more. If you were setting maxhap unnecessarily
      high to avoid recompiling, you may perceive some speedup.

   -- The code can now handle more than 31 alleles at a numbered allele
      locus. It still can't handle more than 31 alleles at a binary factors
      locus. More than 31 liability classes or quantitative trait classes
      have not been a problem.

   -- The parallel code can now handle data sets with an arbitrary number 
      of loops.


   -- The constant MAXWORKINGSET was eliminated from the parallel code.
      The net effect is to save space in most cases, and reduce the
      need for recompilation in some.

See the file README.updates for more details on recent code changes in 
FASTLINK. 

There are many people to thank for their recent help in the FASTLINK project.
Thanks to:

Dylan Cooper, Christopher Hoelscher, and Christopher Hyams
for programming assistance.

Lucien Bachner, Les Biesecker, Anita Destefano, Lynn Goldin,
Ramana Idury, Kimmo Kallio, Cathryn Lewis, Ken Morgan, 
Scot Stenroos, Jim Tomlin, Gerard Tromp for beta testing version 3.0P.

Jeff O'Connell and Joe Terwilliger for pointing out the 31-allele limitation.

Lucien Bachner for pointing out that UNKNOWN did not detect errors
in looped pedigrees.

Please address any comments or questions about FASTLINK to me at:
schaffer at nchgr.nih.gov. 




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