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Dear Colleauge,
Thank you for your interest in MAPMAKER. We are currently distributing:
- MAPMAKER/EXP Version 3.0 - A program for genetic linkage analysis
- MAPMAKER/QTL 1.1 - A program for mapping genes underlying complex traits
- A complete manual for the above with tutorial and reference section
Collectively, we refer to this package as "MAPMAKER". This letter describes:
(0) What is MAPMAKER?
(1) How to Get MAPMAKER
(2) How to Run MAPMAKER on a PC Compatible Running DOS
(3) How to Run MAPMAKER on a Sun SPARCStation Running SunOS
(4) How to Run MAPMAKER on a Apple Macintosh Running A/UX
(5) License Agreement
(0) WHAT IS MAPMAKER?
MAPMAKER/EXP is a linkage analysis package designed to help construct primary
linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP
performs full multipoint linkage analysis (simultaneous estimation of all
recombination fractions from the primary data) for dominant, recessive, and co-
dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only
successor to the original MAPMAKER program.
MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map
genes controlling polygenic quantitative traits in F2 intercrosses and BC1
backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL
can be found in the technical report (included with MAPMAKER/QTL).
For more information on these programs, see the list of references, provided at
the end of this document. Also, be sure to read the technical reports, which
provide tutorials and reference manual for the two programs.
New features in this release include:
- Many many bug-fixes, feature, and user-interface improvements.
- A sophisticated algorithm for detecting typing errors in data from
experimental crosses (see Lincoln and Lander, "Systematic Detection of Errors
in Genetic Linkage Data" Genomics 14: 604-610)
- The ability to draw genetic maps (in MAPMAKER/EXP) and LOD-score plots (in
MAPMAKER/QTL) as PostScript files.
- Support for additional cross types, including F2 intercross, BC1 backcross,
F3(self) intercross, and sib and self mated Recombinant Inbreds in
MAPMAKER/EXP.
- Many features for automating analysis and storing results, particularly
useful with very large data sets. An outline of a database interface is
provided, for sites who wish to integrate MAPMAKER into their informatics
systems.
- New "three point" and "join haplotypes" features for speeding lengthy
analyses.
- A new license agreement which allows free redistribution of MAPMAKER.Under
specific conditions, you may even distribute modified versions of MAPMAKER.
See the license agreement (below) for details.
(1) HOW TO GET MAPMAKER
We distribute ready-to-run executables for any of the following:
- 386 and 486 based PC-compatible computers running DOS 5.0
- High-end Apple Macintoshes running A/UX 3.0, Apple's Unix
- Sun SPARCStations running SunOS 4.x (Sun's Unix)
We will send 3-1/2" high-density (1.44 MB) floppy disks with a photocopied
manual if you send your name, title, organization, address, Internet E-mail
address (if available and if you really use it), FAX (otherwise), to:
MAPMAKER
c/o Dr. Eric Lander
Whitehead Institute for Biomedical Research
9 Cambridge Center
Cambridge, Massachusetts 02142 USA
FAX 617-258-6505
Internet: [email protected] <= NOTE NEW EMAIL ADDRESS!
Bitnet: mapm@mitwibr
Be sure to specify whether you want the PC, SUN, or A/UX version. Do not send
blank disks. We prefer lab heads or PI's to request the program, simply
because these individuals tend to move less often, and contacting the lab
becomes a bit easier for us. Due to the expense involved, please do not request
extra copies of the manual or floppy disks: the license agreement allows to
make extra copies for yourself. An order form is included at the end of this
document.
Alternatively, you can retrieve the software yourself over the Internet via
anonymous FTP from host "genome.wi.mit.edu" in the /distribution/mapmaker
directory. Fetch the FTP.ME (text) file there for further instructions. If you
do get MAPMAKER this way (or already have), please "register" by sending us the
information requested above to the address above, mentioning that you already
have the software. In return, we will send you a printed copy of the manual.
Source code (in "C") is also available by anonymous FTP which you may be able
to compile and run on other platforms.
MAPMAKER for Macintosh, also called MAPMAKER-II (not to be confused with
MAPMAKER Version 2.0) is also available. This program is actually a port of
MAPMAKER 1.0 (circa 1988) to the native Macintosh operating system (that is, it
does not require A/UX) and it is extended with additional graphics
capabilities. This program is the result of a collaboration between The
Whitehead Institute and Dupont Co., and it is distributed by Dupont.
MAPMAKER/QTL is not included. For information, contact:
Mapmaker for Macintosh
c/o Dr. Scott Tingey
E 402/4249
Dupont Experimental Station
Wilmington, Delaware 19898 USA
Below, we describe what sort of computer you will need to run MAPMAKER 3.0 and
MAPMAKER/QTL 1.1.
(2) HOW TO RUN MAPMAKER ON A PC COMPATIBLE RUNNING DOS
In the last 1-2 years, extremely powerful IBM PC compatible computers have
become very inexpensive and widely available. These computers are now an
excellent choice for running MAPMAKER and MAPMAKER/QTL.
To run MAPMAKER on a PC with DOS, your PC must have a 386 or 486 processor, and
should be running MS-DOS 5.0 (that is, we have not tested the program on any
other versions of DOS). We strongly recommend using a math coprocessor - 486DX
and 486DX2 based systems always have such a coprocessor built in, all other
systems (386SX, 386DX, 486SX) require this as an option. For performance
reasons, we do not recommend using a 386SX or SLC. MAPMAKER works correctly
with, but does not make much use of (and does not require) Windows 3.1.
MAPMAKER will need at least 5MB (megabytes) or more of EXTENDED (not EXPANDED)
memory available. More memory is better. You will also need up to 20MB of
free disk space on your hard drive. While the MAPMAKER executable programs and
sample data files should only fill up about 2MB, running the program will
require a large amount (about 16 MB) of "swap space" on your hard disk while it
is running. Your data files and output will take up additional disk space also.
MAPMAKER is sent on 3-1/2 inch high-density (1.44MB) floppy disks. You will
need a computer with this type of drive to install MAPMAKER. Of course, this
does not have to be the computer you eventually run MAPMAKER on, if you have
some other way of transferring the files. MAPMAKER is distributed as an
executable program: you do NOT need a compiler to install it.
Please ask your computer support people if your PC is appropriate. Our test
configuration is a DELL 433P (33MHz 486DX) with 16Mb memory, a 105Mb hard disk,
and a VGA display. We run DOS 5.0 as shipped by Dell, using only the included
utilities, except for Sun's PC-NFS with a 3Com ethernet board. MAPMAKER should
run fine on most PC's (including laptops) with the required features.
MAPMAKER 3.0 draws graphic images in the standard PostScript (Level 1) format.
For your convenience, we have included a copy of the Free Software Foundation's
"GhostScript" package -- a PostScript interpreter which allows you to display
these graphics under Windows 3.1 (GhostScript can also output directly to a EGA
or VGA monitor, although the type is so small as to be illegible). These
PostScript files should also print as-is on any PostScript printer, such as an
Apple LaserWriter, and GhostScript claims it can print these files on a HP
LaserJet or Deskjet or Epson 9-pin or 24-pin compatible printer. We cannot
vouch for these capabilities nor can we provide any support for using
GhostScript as it is not our product. Some commercial products (such as
"Freedom of Press") also claim to accomplish the same thing.
Typical mail order prices for a system like ours are around US$2500 as of the
fall of 1992. Most users will not need quite as fancy (or as expensive) a
computer, however. We cannot attest to MAPMAKER's ability to run on any other
hardware or software configuration.
MAPMAKER is incompatible with some TSRs and device divers. Among others, it
will not work correctly with STACKER.
(3) HOW TO RUN MAPMAKER ON A SUN SPARCSTATION RUNNING SUNOS
Most of our development is done on Sun and DEC Unix-based workstations. The
"RISC" technology they employ makes these machines extremely fast, and many
models are well under $10,000 in the US. The newest low-end systems start at
less than $5,000, and are even cheaper if you are eligible for educational or
US government pricing. Moreover, a good deal of other genome related software
and databases are becoming available for these machines. However, they are more
difficult to set up and maintain than PCs or Macs.
To run MAPMAKER on a Sun Workstation, you will need a SPARC based system
(SPARCStation or Sun-4 system) running SunOS 4.1.x, also known as Solaris 1.0
or 1.1. We have not tested the programs on any other versions of SunOS,
including SunOS 4.0.x or Solaris 2.0 or 2.1, although Sun *claims* they are
binary compatible. Note that some of the new Sun Workstations REQUIRE Solaris
2.1. We also have no experience with non-Sun SPARC compatibles.
MAPMAKER itself requires between 10-30MB (megabytes) of swap space (virtual
memory), depending on the size of your data sets and the number of other
programs you wish to run at the same time. 8MB of physical memory is usually
adequate for MAPMAKER, although 16MB is often recommended. In our experience,
if you run MAPMAKER with Sun's OpenWindows product, you will need *much more*
memory and swap space - we usually recommend 32MB of swap space with at least
16MB of physical memory. Ask a Unix system administrator or Sun technical
support if your computer is appropriate.
MAPMAKER is sent on 3-1/2 inch high-density (1.44MB) "bar" format floppy disks.
You will need a Sun with this type of drive to install MAPMAKER. Of course,
this does not have to be the Sun you eventually run MAPMAKER on, if you have
some other way of transferring the files. MAPMAKER is distributed as an
executable program -- you do NOT need a compiler to install it.
The executable program and sample data files should only fill up 2MB of disk
space, although your data files and output will take up additional disk space.
Unfortunately, SunOS itself uses a lot of disk space: Sun's 400MB drives
provide more than adequate room, although the 200MB drives are a bit of a
squeeze if you actually want to *do* anything with the computer (and you have
no networked file server available).
MAPMAKER is a text based program which runs using a standard terminal
(including a Mac or PC acting as a terminal, connected to the Sun either using
Ethernet or a standard serial line - consult your computer support people or
Sun technical support for details). In principle, this way one SPARCStation
could provide analysis services for an entire lab of Macs and PCs. MAPMAKER
also works in a Command Tool, Shell Tool, or xterm window under SunView,
OpenWindows, or The X Window System.
MAPMAKER draws graphic images in the standard PostScript (Level 1) format. For
your convenience, we have included a copy of the Free Software Foundation's
"GhostScript" package -- a PostScript interpreter which allows you to display
these graphics under X-Windows and OpenWindows. GhostScript works either on the
SPARCStation graphics console itself, or remotely over Ethernet using X-Windows
from a PC, Mac, X-Terminal, or another workstation: ask a Unix system
administrator or Sun technical support for details. These PostScript files
should also print as-is on any PostScript printer, such as an Apple
LaserWriter. However, we have no experience with any other type of printer,
including the Sun "SPARCprinter" or others driven by Sun's "NewsPrint" package.
(4) HOW TO RUN MAPMAKER ON AN APPLE MACINTOSH RUNNING A/UX
MAPMAKER 3.0 and MAPMAKER/QTL 1.1 do not presently work correctly with the
standard Macintosh operating system. The MAPMAKER programs are computationally
intensive large memory model programs which, when ported naively, frequently
crash the stock Macintosh operating system. Unfortunately, this is a difficult
problem to solve (any volunteers out there?). As we mentioned above, a well
ported version of MAPMAKER Version 1.0 is available from Dupont, which will
fill some users' needs.
It is possible, however, to run the newest versions of MAPMAKER (3.0) and
MAPMAKER/QTL (1.1) on Macintoshes running Apple's Unix Operating System, A/UX
3.0. A/UX 3.0 is a merger of the ordinary Macintosh System 7 Finder with a
nearly-invisible (to the user) set of Unix internals. In fact, A/UX users may
almost never know that their computer is running Unix -- they will see only the
ordinary Macintosh Finder and will have access to almost all standard System 7
compatible programs and files. At the same time, A/UX provides the necessary
underlying features for big programs like MAPMAKER and MAPMAKER/QTL to work
without extensive modifications.
In our experience, we found A/UX fairly easy to set up, well documented, and
robust. Moreover, Apple provides telephone support to help install A/UX. Thus,
we can certainly recommend this platform for running MAPMAKER and MAPMAKER/QTL,
with the only caveats that (i) it requires a relatively expensive Macintosh and
other hardware, (ii) A/UX itself is not cheap; and (iii) even the top of the
line Macintoshes cannot compete in price-to-performance with either PC clones,
or most dedicated Unix workstations.
A/UX places significant demands on a Mac. The minimum A/UX 3.0 configuration
needed to run MAPMAKER (as well as System 7 and most other Mac programs) will
take up over 60 megabytes (Mb) of disk space (a full A/UX installation requires
160Mb, although you will likely not need all of these features). Fortunately,
it is possible to load A/UX (and MAPMAKER) onto a second external disk drive.
A/UX requires 8Mb of memory, although 16Mb is preferable for running MAPMAKER
on typical data sets. A/UX only runs on MacII and better class machines (and
original MacIIs will require a hardware upgrade), and A/UX will not run on
PowerBooks. We have run MAPMAKER under A/UX on a Mac IIci (with a minimal A/UX
configuration on an external 80Mb disk, leaving about 20Mb free) and on a
Quadra 700 with 230Mb of disk (full setup, leaving about 100Mb free). Both have
20Mb of memory and Radius monitors and video cards, as well as third-party disk
drives (both worked, although the Quadra was noticeably faster). We cannot
vouch for any other configuration, so consult your Apple dealer (Classic-II's,
LC-II's and IIsi's are probably not a good idea, both because they have no math
coprocessors, and because they have other performance bottlenecks internally).
Most third party hardware is compatible, although you should check with the
vendor. Notorious for compatibility problems are some Ethernet boards and a few
third party CD-ROM drives (in particular, those with NEC mechanisms).
A/UX is available directly from Apple to US Customers (1-800-795-1000) for
$649, and comes with one year of free phone support. A/UX is also available (at
a somewhat lower price actually) from authorized Apple dealers, both inside and
outside of the US. A/UX comes on a CD-ROM, and thus a CD-ROM drive is required
to install it (although you do not need the CD-ROM to subsequently run A/UX -
you can simply borrow a CD-ROM drive to do the installation). A/UX is also
available pre-installed on new Macs. Installing A/UX will require you to back
up all of your files, as it must re-initialize your hard disk (although, if you
have multiple hard disks, it needs only to reinitialize the disk that A/UX is
installed on). The entire installation process took us an afternoon.
MAPMAKER for A/UX is sent on 3-1/2 inch high-density (1.4MB) Mac floppy disks.
You will need a Mac with this type of drive to install MAPMAKER. Of course,
this does not have to be the Mac you eventually run MAPMAKER on, if you have
some other way of transferring the files. MAPMAKER is distributed as an
executable program -- you do NOT need a compiler to install it.
MAPMAKER is a text based program which runs using a standard terminal window
(including the A/UX CommandShell application, which runs under A/UX's System 7
Finder). In principle, you can use one A/UX Mac to serve an entire lab, with
other Macs or PCs acting as terminals, connected to the A/UX Mac either using
Ethernet or a standard serial lines - consult your computer support people or
Apple dealer for details. MAPMAKER does not require the use of MacX or A/UX's
X-Windows implementation, although it will work with it.
MAPMAKER draws graphic images in the standard PostScript (Level 1) format.
These PostScript files should print as-is on any PostScript printer, such as an
Apple LaserWriter NTR (A/UX prints to LaserWriters via AppleTalk, which can be
shared with other Macs as usual). They will not print on an non-PostScript
laser-printer (including the Apple LS) or on an ImageWriter. We do not
presently provide software to view these graphics on the screen or to paste
these graphics into other Mac software.
(5) LICENSE AGREEMENT
The MAPMAKER package, including both the MAPMAKER version 3.0 and MAPMAKER/QTL
version 1.1 programs, all associated files, source code, and documentation
(herein referred to collectively as MAPMAKER) are distributed under the
following license terms at no charge. Installation of the program on any
computer or any use of the program implies that the user and the user's
organization (herein referred to as "you") agree to the following terms:
(1) Warranty, or lack thereof: These programs are provided on an "as is"
basis, with no warranty of any type, including warranty of suitability for any
particular purpose or ability to function correctly on any type of computer. No
technical support can be guaranteed.
(2) Right to Use: You are provided with a license to use MAPMAKER for "basic
research purposes" as defined by the Whitehead Institute for Biomedical
Research. Generally speaking, most mapping efforts are considered "basic
research" unless the sale of either mapped markers or (putative) genes or the
sale of mapping services using the MAPMAKER programs is involved. Also
generally speaking, the sale of particular lines or strains developed through
the indirect use of the MAPMAKER programs is granted. Commercial groups should
consult us as to the specific the legalities covering the use of MAPMAKER for
their project(s). We will work out licensing such efforts on a case by case
basis, and our intention is to see such agreements worked out and to do so
quickly.
(3) Redistribution Rights: The Whitehead Institute grants you permission to
copy MAPMAKER, both for distribution to individuals within your organization
and to those outside the organization. However, all of the software, files, and
documentation must be provided and the software must be copied in its entirety
preserving, among other things, copyright notices, credits, and license
agreement. (One reason behind this is that MAPMAKER and MAPMAKER/QTL are a
synchronized distribution, and only versions of the software, documentation,
and other files delivered together from the Whitehead Institute are guaranteed
to work with each other.) You may charge a small fee for the media and the
physical act of copying the software and documentation, not to exceed US$250,
but all persons who receive the software do so under this license agreement
alone and thus you may not charge for the software itself or restrict any
recipient's right to further distribute the version you give to them.
(4) Modification Rights: The Whitehead Institute grants you permission to
modify MAPMAKER and to distribute modified versions, both to individuals within
your organization and to those outside your organization. However, you must (a)
preserve all of the original copyright notices, license agreement, and credits
in both the software and documentation, (b) add your own notice, making it
immediately apparent upon running the program that it's a modified version, (c)
include the unmodified version in its entirety (as described above) along with
the modified version; (d) distribute the modified version under the same
licensing conditions as the original (e.g. under this agreement); and (e)
notify us in writing that you are distributing a modified version and provide
us with full source code to the modified version immediately upon request.
These restrictions may be waived in some cases by The Whitehead Institute --
contact us for details. Note that this agreement prohibits selling even
modified versions of the MAPMAKER package without our permission. Modified
versions of MAPMAKER distributed for internal use only within a specific
organization are not subject to terms (c), (d), and (e), above.
(6) REFERENCES FOR MAPMAKER AND MAPMAKER/QTL:
E. Lander and P. Green. (1987) Construction of Multilocus Genetic Maps in
Humans. Proc. Nat. Acad. Sci. USA 84: 2363-2367.
E. Lander, P. Green, J. Abrahamson, A. Barlow, M. Daley, S. Lincoln, and L.
Newburg. (1987) MAPMAKER: An Interactive Computer Package for Constructing
Primary Genetic Linkage Maps of Experimental and Natural Populations. Genomics
1: 174-181.
E. Lander and D. Botstein. (1989) Mapping Mendelian Factors Underlying
Quantitative Traits Using RFLP Linkage Maps. Genetics 121: 185-199.
A. Paterson, E. Lander, S. Lincoln, J. Hewitt, S. Peterson, and S. Tanksley.
(1988) Resolution of Quantitative Traits into Mendelian Factors Using a
Complete RFLP Linkage Map. Nature 335: 721-726.
S. Lincoln and E. Lander. (1992): Systematic Detection of Errors in Genetic
Linkage Data. (1992) Genomics 14: 604-610.
A Few Examples:
C. Stuber, S. Lincoln, D. Wolf, T. Hellentjaris, and E. Lander. (1992)
Identification of Genetic Factors Contributing to Heterosis in a Hybrid from
two Elite Maize Inbred Lines. Genetics, 132: 823-839.
H. Jacob, K. Lindpaintner, S. Lincoln, K. Kusumi, R. Bunker, Y. Mao, D. Ganten,
V. Dzau, and E. Lander. (1991) Genetic Mapping of a Major Gene Causing
Hypertension in the Stroke Prone Spontaneously Hypertensive Rat. Cell 67: 213-
224.
W. Dietrich, H. Katz, S. Lincoln, M. Daly, H. Shin, J. Friedman, N. Dracopoli,
and E. Lander. (1991) A Genetic Map of the Mouse Suitable for Typing
Intraspecific Crosses. Genetics 131: 423-427.
A. Paterson, J. Hewitt, S. Peterson, S. Lincoln, E. Lander, and S. Tanksley.
(1991) Mendelian Factors Underlying Quantitative Traits: Comparison across
Species, Generations, and Environments. Genetics 127: 169-179.
N. Dracopoli, B. Stanger. C. Ito, K. Call, S. Lincoln, E. Lander, and D.
Housman. (1988) A Genetic Linkage Map of 27 Loci from PND to FY on the Short
Arm of Human Chromosome 1. American Journal of Human Genetics 43: 462-470.
How to cite MAPMAKER/EXP 3.0 or MAPMAKER/QTL 1.1:
Please use Lander et al. 1987 for MAPMAKER/EXP, and Paterson et al. 1988 for
MAPMAKER/QTL. Please also cite:
S. Lincoln, M. Daly, and E. Lander: Constructing Genetic Maps with MAPMAKER/EXP
3.0. (1992) Whitehead Institute Technical Report. 3rd edition.
S. Lincoln, M. Daly, and E. Lander: Mapping Genes Controlling Quantitative
Traits with MAPMAKER/QTL 1.1. (1992) Whitehead Institute Technical Report. 2nd
edition.
Ver 3b, 12/92
MAPMAKER/EXP 3.0 and MAPMAKER/QTL 1.1 Request:
Print Name ____________________________________________________________________
Title _________________________________________________________________________
Organization __________________________________________________________________
Address _______________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
Phone _________________________________________________________________________
FAX _________________________________________________________________________
Electronic Mail _______________________________________________________________
[ ] Internet [ ] Bitnet
Select Either:
____ (1) Version for Sun SPARCStations Running SunOS 4.1.
____ (2) Version for IBM PC-Compatibles Running DOS 5.0.
____ (3) Version for Apple Macintosh Computers Running A/UX 3.0.
____ (4) Manual Only (for those who retrieved the software by FTP).
All formats include 3-1/2" high density (1.44Mb) floppy disks with executable
code and printed documentation. Source code is available by anonymous FTP.
Return This To:
MAPMAKER
c/o Dr. Eric Lander
Whitehead Institute for Biomedical Research
9 Cambridge Center
Cambridge, Massachusetts 02142 USA
FAX 617-258-6505
For Information on MAPMAKER 1.0 for Macintosh:
Mapmaker for Macintosh
c/o Dr. Scott Tingey
E 402/4249
DuPont Experimental Station
Wilmington, Delaware 19898 USA