From: ftp-bimas.cit.nih.gov                         Last Mod: March 14, 1996

              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.


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.

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

Similarities:
1. DOS FASTLINK is essentially the same as FASTLINK 3.0P, provided that
   the computer does not crash during the run.
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 Columbia.

Differences:
1. We are distributing executable versions for DOS FASTLINK, rather
   than source as for UNIX FASTLINK. Details about how to get the executables
   are given below.
2. The source code for FASTLINK for DOS is the same as the non-DOS source
   code. However, if you wish to get source code and compile it, you
   should use the djgpp C compiler; this is a port of the gcc compiler
   to DOS. Instructions for retrieving and installing the compiler are
   in README.djgpp. djgpp is freely available over the Internet by ftp.
3. DOS FASTLINK does not support crash recovery.
4. We are distributing only the "slow" versions of FASTLINK for now.
   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 code was tested on several
different 486 machines. I am fairly certain that it won't work on
286 and below machines.

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

5. We strongly recommend trying the programs outside of Windows
(i.e., in vanilla DOS) first. They probably work from Windows too,
but it may be the case that the compiler makes some assumptions
about how the video/monitor environment is set up, which are
not consistent with the setup of your machine.

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

Here are the instructions for retrieving the code:
   ftp softlib.cs.rice.edu

Login as anonymous and leave your full e-mail address as password.
   cd pub/fastlink/dos
   binary

In that directory 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 executables are not currently included in fastlink.tar.Z,
so you must retrieve them as individual files.






