From: ftp-bimas.cit.nih.gov                         Last Mod: Sep. 30, 2006

              FASTLINK for DOS

This file describes FASTLINK for DOS, especially how it is
related to FASTLINK for UNIX. Thanks to Ramana Idury and Roger Kou
for figuring out how to convert the UNIX versions to
DOS versions initially. Thanks to Aleksandr Morgulis for help
in 2006 with making new compilations with Visual C++ for
newer versions of Windows.


Fundamental: We distribute 5 executables
    
      ilink.exe
      linkmap.exe
      lodscore.exe
      mlink.exe
      unknown.exe

These can be plugged in directly instead of the similarly-named
LINKAGE for DOS executables. An easy way to do this is to have
separate directories for LINKAGE and FASTLINK. If you put the
FASTLINK directory ahead of the LINKAGE directory in your default
path, DOS will find the FASTLINK executables when appropriate,
and will continue to use the LINKAGE executables for
the auxiliary programs: lcp, lsp, lrp, makeped, preplink.

Older executables are in the pub/fastlink/dos directory.
Newer executables are in the pub/fastlink/windows directory.

Some fundamental similarities and differences between UNIX versions
and DOS versions should be noted:

Similarities:
1. The old executables are essentially the same as FASTLINK 3.0P; while
   the new executables are essentially the same as FASTLINK 4.1P.
2. Most of the documentation still applies except the instructions for
   installation (we distribute executables for DOS, so no compilation
   is required) and portability (basically irrelevant to DOS).
3. We are distributing versions of LODSCORE, ILINK, LINKMAP, MLINK, UNKNOWN.
   Other auxiliary programs can be obtained from the FTP site at 
   Rockefeller University.

Differences:
1. We are distributing executable versions for DOS/Windows, rather
   than source as for UNIX FASTLINK. Details about how to get the executables
   are given below.
2. FASTLINK for DOS/Windows does not support crash recovery.
3. We are distributing only the "slow" versions of FASTLINK.
   These are still measurably faster than LINKAGE.

Cautions:
1. FASTLINK is derived from LINKAGE 5.1 for UNIX and not from LINKAGE for
DOS. We have tested FASTLINK on DOS, but we have not investigated to
what extent LINKAGE for UNIX and LINKAGE for DOS are incompatible.

2. If FASTLINK and LINKAGE give different answers, you should not
assume that FASTLINK is wrong. LINKAGE may be wrong.
I have fixed 2 significant bugs in LINKAGE LODSCORE/ILINK and 1
significant bug in LINKAGE LINKMAP/MLINK. These bug fixes are described
in README.updates. There is also an inconsistency in scaling in
LINKAGE LINKMAP, which is fixed in FASTLINK LINKMAP (see README.scaling).

3. You must a have 386 or higher machine. The executables under
the pub/fastlink/dos directory  were tested on several
different 486 machines. The executables under the pub/fastlink/windows
directory were tested in 2006 on a PC running a fairly recent
version fo Windows.

4. You should have a Math co-processor on the machine.
Most recent 486 machines will have this.

Like FASTLINK for UNIX and VMS, FASTLINK for DOS is distributed by FTP
from a computer at NIH.  Contact me by
e-mail at schaffer@helix.nih.gov if you want the executables mailed
to you on floppy disks.

Here are the instructions for retrieving the code:
   ftp fastlink.nih.gov

Login as anonymous and leave your full e-mail address as password.
   cd pub/fastlink  [for new versions]
   binary

In that directory and the
   windows
subdirectory you will find various files. You may wish to
retrieve all the files with the name README and all the files that
end .ps. These are all relevant documentation files.
The file README with no extension gives a roadmap to
all FASTLINK documentation.

[For those who  receive FASTLINK for DOS on 3.5" diskettes,
the documentation is on one of the diskettes and the sticky labels tell
you which it is.]

For those who retrieve the files via ftp.
Having retrieved whatever documentation you want, you should retrieve:

   lodscore.exe 
   ilink.exe
   linkmap.exe
   mlink.exe
   unknown.exe

You should retrieve all 5 files. 
You must use the FASTLINK version of UNKNOWN with the FASTLINK
main programs. Remember to use binary mode
in FTP.  Previous versions had a limit on the number of
haplotypes; this limit has been eliminated in FASTLINK 3.0P.


Note: The DOS/Windows executables are not currently included in
fastlink.tar.Z, so you must retrieve them as individual files.






