From: danj@merlot.gwu.edu (Dan Jacobson )
Subject: Re: PD Genetic Mapping Software
Organization: George Washington University, Washington, D.C.
Date: Wed, 11 Nov 1992 18:17:17 GMT

In article <1992Nov10.215921.10509@schaefer.math.wisc.edu> horn@schaefer.math.wisc.edu (Jeffrey Horn) writes:
>Would anyone have any leads on acquiring public domain or at least
>freely available genetic linkage software (for plant populations).
>I am interested in calculating genetic maps, displaying them in 
>MS-Windows or X Windows, and printing the maps.  I am aware of 
>Lander's Mapmaker program, but would like something a bit more
>automatic and a bit more graphical.
>
>Thanks for your help, 
>
>Jeffrey Horn
>.

Here is a summary of responses to a similar request for linkage
software.


Best of luck,

Dan Jacobson

danj@chablis.gwu.edu
    
********************************************************************************

From: "Daniel E. Weeks" <WEEKS@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@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@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@bcm.tmc.edu
	Houston, TX   77030
	------------------------------------------------------------
********************************************************************************

From:         Jurg Ott <OTT@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 variance of an MLE of
theta from three values of theta and its log likelihoods or lod
scores.  The likelihood is approximated by a normal density,
i.e., the log likelihood is quadratic.
     VARCO6 (2.21) approximates means, variances and correlation
for two jointly estimated variables, x and y, from six points
(x,y) and associated likelihood values.
********************************************************************************

         ********************MapMaker Information********************

From: csb@jax.org (Carolyn Blake)
Organization: The Jackson Laboratory, Bar Harbor, ME 04609

Mapmaker is available for other 'not fancy' systems as well. We have it running
under UNIX with no fancy graphics capabilities.

You may also wish to contact Dr. Alan Hillyard (alh@morgan.jax.org). He
maintains GBase, a linkage map database of the mouse, and is currently working
on databases of linkage maps for other species.
********************************************************************************

From: "Gunnell, Mark" <gunnell@fcrfv1.ncifcrf.gov>

We are currently running MapMaker version 1.9 under VMS version 5.4-2, and it
does not require anything beyond standard ascii terminals.  We obtained the
package from:

	MAPMAKER
	Dr. Eric Lander
	Whitehead Institute
	9 Cambridge Center
	Cambridge, MA 02142
	mapm%mitwibr@mitvma.mit.edu

Cost was less than $20.  Let me know if you need additional information.
-------------------------------------------------------------------------------
Mark A. Gunnell                   | Internet: gunnell@ncifcrf.gov
Sci. Applications Analyst         | Bitnet:   gunnell%ncifcrf.gov@cunyvm.bitnet
Advanced Scientific Computing Lab.| Phone:   (301) 846-5779
PRI/DynCorp                       |
NCI-FCRDC                         |
PO Box B, Bldg 430                |
Frederick, MD 21702-1201  USA     |
-------------------------------------------------------------------------------
********************************************************************************

         ********************GeneTree Information********************

From: wijsman@max.u.washington.edu
Subject: GENETREE distribution

GeneTree is finally being released for distribution.  We have finally  gotten a
semi-reasonable agreement on a royaly agreement with the company  which
produced the driver used internally by the program to do the graphics  needed
to print pedigrees.  As a result, GeneTree will be available at  cost to
non-profit and educational institutions for $125, which covers the  cost of the
license for the commercial graphics driver, manuals, diskettes,  mailing, etc.

A description of GeneTree and its history are below.

     The GeneTree 1.0 package provides a convenient way to draw family
tree diagrams suitable for genetics or geneology using an IBM PC or
compatible computer.  The package consists of the GeneTree program, which
draws pedigree diagrams using a command language, and SC, a menu-driven
program that facilitates creation of GeneTree commands.  GeneTree and SC
are made available with program manuals, examples of family tree diagrams,
and a GeneTree Quick Reference Guide.  GeneTree is written in the C
programming language.  Note that it is a DRAWING program and does not
compute genetic parameters.

Technical requirements:  an IBM PC or compatible with 512K or more of
     memory, and a hard disk with at least 500K unused space, and
     DOS 3.0 or greater.

Salient features of the program are:

1) PEDIGREE DISPLAY:  Produces standard pedigree display used in human
        genetics, using standard symbols, with user control over
        arrangement and display of the pedigree, symbol size, and
        placement of text and numeric data around pedigree symbols.
        Over 30 shading patterns, with full or split symbol shading.

2) SPECIAL PEDIGREE CAPABILITIES: Handles within-generation inbreeding
        loops without the need for "doubling" a person for drawing
        complex pedigrees, can display multiple marriages and marriages
        with no offspring, can draw individuals with only one parent
        in the pedigree (dummy parents are not necessary), and will draw
        large pedigrees on multiple pages

3) SIMPLE COMMAND LANGUAGE: Draft pedigrees can be drawn using only
        three commands, and GeneTree will automatically scale diagrams

4) BATCH OR INTERACTIVE MODE: Operates in either batch or interactive
        mode, flexible and simple input file structure, can be combined
        with existing database management of data collection software

5) CURRENT LIMITS: Current maximum pedigree size is about 130 individuals.
        Maximum number of text and/or number fields around any one
        pedigree symbol is 25, with a maximum of 256 characters.

     History of GeneTree is as follows.  Robert Hodges wrote the program
while he was the system manager for the Alzheimer's disease research
center at the University of Washington, partly because of dissatisfaction
with what was available for investigators who were doing genetic analyses.
In particular, there was nothing at the time at low cost or no cost which
could easily interface with the kinds of databases collected in the context
of genetic analysis, and which could be used in the context of a variety
of analyses to draw pedigrees of varying size and complexity during
different stages of the analyses.

     In order to make it possible to print pedigrees on a variety of
printers/plotters, Robert decided to use a commercial driver package.
This allows pedigrees to be printed on most if not all printers
which are compatible with IBM PCs.  The side effect of the use of the
driver package, however, is that if we distribute the package, we must
pay royalties on the driver.  This is why it has taken so long to
distribute the program; negotiating lower royalties and coming up with a
mechanism to collect royalties was not easy!

     I have found the program to be extremely useful in my work, which
requires examining genetic marker data on pedigrees, constructing
haplotypes for multi-site data, using  sequential sampling to collect
pedigrees which have a trait of interest, etc.  Most of these
uses involve printing out the same pedigree on a frequent basis with
different data, and involve regular interaction with a database.
I am the official contact person for furthers inquiries and/or
to request a copy of the package.

	Ellen Wijsman
	wijsman@saam.bioeng.washington.edu
	or
	wijsman@max.washington.edu
	RG-25
	University of Washington
	Seattle, WA   98195
********************************************************************************