Linkage , Mapmaker

Dan Jacobson danj at merlot.gwu.edu
Wed Oct 21 15:36:00 EST 1992


Antonio R. Franco writes:

>Where are the sources to get the programs Mapmaker and Linkage used for
>a mapping project?. I am interested in both the PC and Macintosh version.
>Thank you for your courtesy


Below is a summary of information received from a similar question on a
different newsgroup (probably more than you ever wanted to know about
this type of software :-).  I believe that Stephen Thompson originally put 
this together - I saved it and now shamelessly redistribute it as a Linkage 
FAQ.

Happy hunting,

Dan Jacobson

danj at chablis.gwu.edu



*******************************************************************************

********************************************************************************

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)
  6  Linkage Utility programs, source and compiled for OS/2 (see
     list at the end) [1 DD disk]
  7  NOCOM program for analysis of mixture of distributions. In-
     cludes the COMPMIX and HIST programs.  FSC
  8  Linkage Utility programs, source and compiled for DOS [1 DD
     disk]
  9  PC-LIPED (two-point linkage analysis, up to 5 alleles per
     locus), version Oct. 1988.  Includes SEXLODS program for
     approx. separation of male and female recombination frac-
     tions.  FSC
 9a  LIPED, same as disk 9 except that up to 6 alleles per locus
     are allowed and program requires more memory to run.
 10  PC-WRITE version 3.02 text editor for data entry (Quicksoft,
     Inc.)  [3 disks, 10a-10c]
 14  Programs for homogeneity tests, source and compiled for OS/2
     with coprocessor  [1 DD disk]
 15  same as #14 but compiled for DOS, no coprocessor required [1
     DD disk]
 16  same as #14 but compiled for DOS, coprocessor required [1 DD
     disk]
 17  Kermit V2.30 program for electronic communication.
 18  LIPEDMAX program version Nov. 1987 for iterative estimation
     of age of onset parameters (lognormal distribution of age at
     onset).  FSC
 20a SLINK simulation program, DOS and OS/2 version, Prospero
     Pascal source code, documentation, and examples [1 DD disk]
 20b SLINK compiled for DOS with coprocessor  [1 DD disk]
 20c SLINK compiled for DOS not requiring coprocessor [1 DD disk]
 20d SLINK compiled for OS/2, requiring coprocessor [1 DD disk]
 20e SIMULATE program for simulation under no linkage (DOS, OS/2,
     and VAX, source and compiled)  [1 DD disk]
 21  SLINK simulation program, VAX VMS source code  [1 DD disk]
 22a LINKAGE programs for 2-locus disease models (TMLINK, TLINKM,
     TILINK), source and compiled for DOS requiring coprocessor
     [1 HD disk]
 22b same as #22a but for VAX VMS, source  [1 DD disk]
 22c same as #22a but compiled for OS/2, requiring coprocessor [1
     HD disk]
---------------------------------------------------------------

We keep a list of people who ordered programs from us and/or who have taken our
linkage courses.  These individuals regularly receive the LINKAGE NEWSLETTER
which is so far being mailed free of charge a few times a year.

                  LITERATURE (for information purposes only)

     J. Ott: "Analysis of Human Genetic Linkage", revised edi-
tion. Johns Hopkins University Press, Baltimore and London, 1991
($47.50).  Japanese translation of original edition by Soft
Science, Tokyo, 1987.
     E.A. Thompson: "Pedigree Analysis in Human Genetics", Johns
Hopkins University Press, Baltimore and London, 1986 ($35).
     K.E. Davies (editor): "Human Genetic Diseases - A Practical
Approach". IRL Press, Oxford England and Washington, D.C., 1986
($25, softbound; $40, hardbound).

     PROGRAMS CONTAINED ON DISKS 6 and 8 (version no. in paren-
theses)

     2BY2 (1.0) carries out Fisher's exact test in 2x2 tables
(n<5000).
     ASSOCIATE (2.3), for two loci with codominant alleles,
partitions the chi-square for phenotypic association into two
components, (1) due to allelic association, (2) other phenotypic
association.
     BINOM (1.63) calculates binomial probabilities and confi-
dence intervals (n<5000).
     CHIPROB (2.2) computes p-values (upper tail probabilities)
for the chi-square distribution.
     CONTING (2.4) calculates chi-square for contingency table
data.
     EQUIV (2.6) calculates equivalent fully informative observa-
tions from a lod score curve.
     HIST (2.3) produces a histogram.
     MAPFUN (2.31) converts recombination fractions into map
distances (6 mapping functions) and vice versa.
     NORINV (1.31) accurately computes the normal deviate from a
given tail probability.
     NORPROB (3.2) accurately computes the tail probabilities (p-
values) associated with a normal deviate, x.
     PERMUTE (2.3) produces a list of all n!/2 orders of n gene
loci.
     PIC (1.3) computes for given alleles at one locus the PIC
value and heterozygosity.
     RERI (2.2) calculates and combines relative risks from a set
of 2x2 tables and carries out homogeneity tests among the tables.
     VARCO3 (2.41) approximates mean and 


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