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<head>
<title>FASTLINK Home Page</title>
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<td width="360" class="head1" valign="BOTTOM"> <span class="H1">Genetic Analysis Software</span></td>
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<td width="100"><a href="http://www.ncbi.nlm.nih.gov/Entrez/" class="BAR">Entrez</a></td>
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<p>
<span class="GUTTER1">Downloads</span>
<br>
<br>
<a href="ftp://fastlink.nih.gov/pub/fastlink/fastlink.tar.Z" class="GUTTER2">FASTLINK package</a>
<br>
<br>
<a href="ftp://fastlink.nih.gov/pub/fastlink/README" class="GUTTER2">README</a>
<br>
<br>
<a href="ftp://fastlink.nih.gov/pub/fastlink/README.updates" class="GUTTER2">README.updates</a>
<br>
<br>
<a href="ftp://fastlink.nih.gov/pub/fastlink/unknown.ps" class="GUTTER2">unknown.ps</a>
<br>
<br>
<a href="ftp://fastlink.nih.gov/pub/fastlink/unknown.ps" class="GUTTER2">loops.ps</a>
</p>
<p> </p>
<a href="fastref.html" class="GUTTER1">References</a>
</p>
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<td width="303" bgcolor="#CCCCFF" class="H3"> Overview</td>
</tr>
</table>
<p>
Genetic linkage analysis is a statistical technique used to map
genes and find the approximate location of disease genes.
There was a standard software package for genetic linkage
called LINKAGE. FASTLINK is a significantly modified and
improved version of the main programs of LINKAGE that
runs much faster sequentially, can run in parallel, allows
the user to recover gracefully from a computer crash, and
provides abundant new documentation. FASTLINK has been
used in over 400 published genetic linkage studies.
</p>
<p>
Version 1.0 of FASTLINK was first distributed in May 1993.
We are now up to version 4.1P, first released in July 1999. You
can download the current version with all documentation as
well as some individual documentation files by following
the hyperlinks on the left-hand side of this page. When
you retrieve FASTLINK as a whole, you will get 1 file called
fastlink.tar.Z. To unpack the archive on a UNIX machine, issue
the commands
<pre>
uncompress fastlink.tar.Z
tar -xvf fastlink.tar
</pre>
Users who do not have access to <tt>uncompress</tt> and <tt>tar</tt>
equivalents can get the entire distribution piecemeal by ftp'ing to
the server fastlink.nih.gov, logging in as user <tt>anonymous</tt>,
and going to the directory <tt>pub/fastlink</tt>.
Start with the file <tt>README</tt>, which is available by a direct
hyperlink on the left to get a roadmap to all the documentation.
If you want to see whether a new version of FASTLINK contains
improvements that you want, look at the file README.updates, also
available by a single click on the left.
</p>
<p>
The FASTLINK project is directed by
<A href="mailto:schaffer@helix.nih.gov">Alejandro Schäffer</A>.
Over the years, participants in developing FASTLINK and
providing customer service have included: Richa Agarwala (NIH)
Ann Becker (Technion), Robert Cottingham Jr.,
Alan Cox (Rice U.),
<A href="http://www.cs.rochester.edu/u/sandhya">Sandhya Dwarkadas</A> (now at U. Rochester),
Dan Geiger (Technion), Sandeep Gupta (now at Trilogy),
Christopher Hoelscher, Chris Hyams (now at Trilogy),
Ramana Idury (now at Kiva Genetics),
Peter Keleher (now at U. Maryland), K. Shriram (Rice U.)
Willy Zwaenepoel (Rice U.). I am also very grateful to
hundreds of users around the world for comments, questions,
suggestions, and bug reports, and most of all for being bold
enough to try some new software and stick with it.
</p>
<p>
The FASTLINK project has benefited from two interesting
concepts from computer systems. First, K. Shriram implemented
a checkpointing facility that allows the FASTLINK main programs
to recover gracefully from a crash of the underlying computer.
Stephen Rich (now at Wake Forest U.) gets the prize for the most
unusual usage of checkpoint/crash recovery. Just before moving
his workstation from Minnesota to North Carolina, he killed
an ongoing FASTLINK run, and shut down the computer. Once he
and the workstation got installed in North Carolina, he resumed
the run near where it left off and completed it successfully.
I have reused some of K. Shriram's checkpointing code in the
PSI-BLAST module of the widely used
<A href="http://www.ncbi.nlm.nih.gov/BLAST">BLAST</A>
package.
</p>
<p>
Starting with version 2.3P, the ilink, mlink, and linkmap
programs in FASTLINK can run in parallel. What is especially
surprising is that essentially the same code can run on
either shared-memory multiprocessors or on homogeneous
networks of uniprocessors. This feat is made possible by using
the <A href="http://www.cs.rice.edu/~willy/TreadMarks/overview.html"> TreadMarks
</A>
distributed shared memory system developed at Rice University.
</p>
<p>
FASTLINK comes with substantial documentation. Most of
the documentation files are in ASCII text. Two of the more
popular documents that are in PostScript are:
<A href="unknown.html"> The Mystery of (the) Unknown</A>,
which explains the preprocessor program unknown, and
<A href="loops.html"> Loops in FASTLINK </A>. You can download
PostScript versions by clicking on the hyperlinks to the left
or read the documents one page at a time by clicking on the
hyperlinks in this paragraph.
Thanks to many users and especially the student participants
on the FASTLINK projects who kept asking questions that
deserved clear and written answers for everyone's benefit.
</p>
<p>
To promote better understanding of how to do simple
linkage analyses, I teach a class called
<A href="http://bimas.cit.nih.gov/linkage/index.html"> "Cookbook Linkage Analysis, Ab Initio" </A>.
Follow the hyperlink in this paragraph
to get to a page that lets you link to the course overheads
and 11 recipes for different aspects of linkage analysis.
Thanks to Jim Tomlin for putting the course materials on the Web.
</p>
<p>
I maintain a mailing list of FASTLINK users, used mostly to
announce new versions, updates, and bug fixes. If you have retrieved the
code and would like to be on the mailing list, send me e-mail at
<a href="mailto:schaffer@helix.nih.gov">schaffer@helix.nih.gov</a>.
</p>
<p> </p>
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