genetic linkage mapping---summary compilation (long)

[Steve Thompson: VADMS genetics]

Dear Bio-Soft land networkers:

Many grateful thanks are extended to all you classical genetics types who sent
me messages regarding my request for linkage mapping software.  The response
was quite impressive and my associate and myself are most appreciative.

As promised, a summary of the replies to my query (repeated below) has been
compiled and comprises the following text:

my initial query----------------------------------

     Fellow netters:

     An associate of mine is interested in constructing primary linkage maps of
     Mendelian genetic markers in sheep.  She needs to be able to analyze the
     segregation of dominant, recessive and co-dominant traits in known
     pedigrees and experimental crosses.  She has brought the commercial
     package Mapmaker from Whitehead Institute to my attention.  It appears to
     be able to do exactly what she needs, however, it reguires the fancy
     integrated, graphical operating system SCO "Open Desktop."  We are curious
     to find out if there is a less exorbiant alternative available.  Has
     anyone out there heard of any similar mapmaking software with these type
     of capabilities but designed to operate under either standard DOS or
     VAX/VMS?  Naturally public domain ware would be desirable but we are
     interested in anything available at all.  If interests warrant, I will be
     happy to post a summary of replies to the board.

     Thanks in advance, Steve Thompson

the various replies follow------------------------

           ********************General Interest*******************

From:    NWHETT at NCSUMVS.BITNET
 
Just wanted to let you know that I am interested in the replies you receive,
and if you don't summarize and repost the responses, to request that you
forward them to me (nwhett at ncsumvs.bitnet or nwhett at ncsumvs.ncsu.edu). There is
a package of programs (DOS- based) available from a fellow named Jurg Ott at
Columbia that performs some linkage analysis functions. I don't know if it does
mappping in the sense of deriving most likely gene order from three-point
crosses, but it is free and might be worth your time to look into. I don't have
the address off the top of my head, but if you need it, let me know and I can
look it up. Good luck! Ross Whetten
********************************************************************************

From: "Daniel E. Weeks" <WEEKS at vms.cis.pitt.edu>

You may want to try the LINKAGE package.  The DOS version is available from:

	Dr. Jurg Ott 
	Columbia University 
	Box 58 722 West 168th Street 
	New York, NY 10032
	E-mail: ott at nyspi.bitnet

There is also a VAX/VMS or Unix version available from Dr. Mark Lathrop at the
Centre d'Etude Polymorphisme Humain in Paris.  Please let me know if you need
the address.

The LINKAGE package is freely-distributed and is widely used for constructing
linkage maps in humans.  There is also a version designed specifically for
experimental crosses.

An alternate package is also available, called the Programs for Pedigree
Analysis.  This package of programs is available from:

  	Dr. Kenneth Lange
  	Department of Biomathematics
  	University of California Los Angeles
  	School of Medicine
  	Los Angeles, CA 90024-1766

This package is written in FORTRAN and is very easy to port to almost any
machine with a good FORTRAN compiler.  The MENDEL portion of this package has
been used to construct linkage maps in humans (See the most recent issue of the
American Journal of Human Genetics).

	Sincerely, Daniel E. Weeks
 	Department of Human Genetics
 	University of Pittsburgh
********************************************************************************

         ********************Linkage Information********************


From: Robert Cottingham <bwc at mbir.bcm.tmc.edu>

There is a very good alternative if you are familiar with linkage analysis,
computers and programming.  It is the LINKAGE package by Lathrop et al.  It is
available for DOS, VMS and Unix systems.  I would recommend against using it
under DOS for anything but small problems.

To pick up a copy do an anonymous FTP to corona.med.utah.edu (128.110.231.1)
and cd pub/linkage/vms and take it from there.


	------------------------------------------------------------
	Bob Cottingham          	Phone:  713/798-4275
	Cell Biology, M301          	Fax:        790-1275
	Baylor College of Medicine	Email: bwc at bcm.tmc.edu
	Houston, TX   77030
	------------------------------------------------------------
********************************************************************************

From:         Jurg Ott <OTT at NYSPI>

Attached is a list of programs available from us for genetic linkage analysis. 
The LINKAGE program set is probably suitable for the analysis of those sheep
families. These programs are what most people in human linkage analysis use
nowadays.  I currently distribute only the PC version.
 
          COMPUTER PROGRAMS USEFUL IN LINKAGE ANALYSIS
 
These programs are designed for IBM type microcomputers, unless indicated
otherwise.

On disks 5a-5c, below, you will find the current PC version (5.10) of the
LINKAGE programs for general and 3-generation pedigrees.  Versions prior to 5.1
are no longer supported by us. A version for OS/2 is also available (disk 4).
     
The HOMOG and Linkage Utility programs are now written in standard Pascal and
compiled with with Prospero Pascal.  Execut able code is available for DOS and
OS/2.
 
               ORDERING INSTRUCTIONS - PLEASE FOLLOW CAREFULLY
 
1. Below, sets of files are arranged as numbered disks. Most of these 'disks'
hold up to 360 KB characters, but some (identified with 'DD') contain up to 720
KB, and some ('HD') contain up to 1.4 MB.  To order programs, send this
pamphlet, with the desired items circled (we will return a new pamphlet).
Enclose the appropriate number of formatted disks to hold the programs desired,
either IBM PC 5-1/4" 360 KB, or high-density 5- 1/4", or 3-1/2" disks (DD or
HD) that we will then return (high-density disks hold several of the items
listed below).  Notice that 360 KB disks will be written on a high-density
drive so that they may not be readable on a low-density drive.  For 3-1/2"
disks, do NOT format a disk labelled DD as a high-density disk.
 
                    ONLY FORMATTED DISKS WILL BE PROCESSED
 
2. Enclose one extra empty disk to help cover postage. 
3. Enclose an address label (possibly self-sticking) with your address on it.
                          
Regular orders---Disks are sent out approximately once a week.  No cost.
 
Rush orders---Disks will be mailed on the day the order is received.  
Handling charges (rush orders only):

     $100 for postal mail, or Express service charged to your account.
     $120 when sent by Federal Express charged to our account.

Forms of payment:  (1) Check made out to Columbia University, enclosed with
your order; or (2) Letter stating that you will pay an invoice sent with the
disks (government purchase order ok).
 
	Katherine Montague/Jurg OTT        Tel. (212) 960-2507
	Columbia University, Box 58
	722 West 168th Street              FAX  (212) 568-2750
	New York, N.Y. 10032
 
 
                  LIST OF AVAILABLE PROGRAMS (see next page)
 
TPS= Turbo Pascal (TP) source code (compiler needed).
TPC= Turbo Pascal, compiled for IBM PC
FSC= Fortran (Microsoft v.4.01), source and compiled.
EXE= executable code
 
Item Contents
----------------------------------------------------------------
LINKAGE programs version 5.10, disk 4 (Prospero Pascal, DOS or
OS/2) and disks 5a-5c (Turbo Pascal version 5, DOS).  The pro-
grams are in compressed form and will have to be decompressed
using a program supplied on disks 4 and 5a.  Printed documenta-
tion (version 5.10, May 1991) will be provided.  Our benchmark
pedigree is on disk 5b (subdirectory BENCH).
 
LINKAGE programs in Prospero Pascal (OS/2 or DOS, compiled for
OS/2 only, for use on machines with or without coprocessor):
  4  All programs and documentation  [1 HD disk]
 
LINKAGE programs in Turbo Pascal (general and CEPH pedigrees;
DOS only):
For general pedigrees order 5a+b, for 3-generation pedigrees
order 5a+c.
 5a  Management and utility programs
 5b  Programs for general pedigrees; benchmark data in \DISK5b\
     BENCH
 5c  Programs for three-generation pedigrees
 
OTHER PROGRAMS (Turbo Pascal version 5 except where noted