4 August 2001 README file for QTL Cartographer. QTL Cartographer is a package of programs that will aid in locating the genes that control quantitative traits using a molecular map of markers. It includes some programs to allow simulation studies of experiments. Where to get QTL Cartographer: Via the web, point your browser to ftp://statgen.ncsu.edu/pub/qtlcart and shift-click on a file to download it. Otherwise, ftp to statgen.ncsu.edu (152.14.14.17) with username: ftp password: your email address cd to /pub/qtlcart ftp> cd /pub/qtlcart This is what's in the directory: ---------------------------------------------------------------- ---------------------------------------------------------------- Filename Explanation ---------------------------------------------------------------- QTLCartWin.zip 32 bit Windows NT/9x version QTLCartUnix.tar.Z Unix distribution QTLCartMac.sea.hqx Macintosh distribution README This file gnuplot.exe MS-Windows version of Gnuplot gnuplot.sit.hqx Macintosh Version of Gnuplot gnuplot.tar.Z Unix distribution of Gnuplot 1.10b/ Version 1.10b 1.12f/ Version 1.12f 1.13g/ Version 1.13g 1.14/ Version 1.14 WQtlSetup.exe Shengu Wang's GUI front-end for Windows data/ Published data sets ChangeLog Changes made in the programs ---------------------------------------------------------------- ---------------------------------------------------------------- **** For MS-Windows 3.1, 3.11 (version 1.12f) Download the files LHARC.EXE and QTLCART.LZH in binary format to your DOS machine. Create a subdirectory for the binaries (say, c:\qtlcart). Move the files to that subdirectory and uncompress the archive QTLCART.LZH with the following command: c:\qtlcart\> LHARC x QTLCART The ten binaries will be uncompressed. Now load Windows and start up the File Manager. Create a program group, say "QTL Cartographer", and drag the *.exe files from the File manager to the new program group. They will then be ready to use with a double click. You will be presented with a menu of options to select. **** For MS-Windows NT/9x: Download QTLCartWin.zip into a subdirectory and uncompress it by double clicking the archive. You may need to download an unzip utility. **** For UNIX: Download the file QTLCart.tar.Z in binary form from statgen.ncsu.edu. It is in the same directory that this file came from. Anonymous ftp into statgen.ncsu.edu and cd to /pub/qtlcart. On your local machine, create a subdirectory for the distribution, then move the file QTLCart.tar.Z to it. Uncompress and untar the file as follows: % uncompress QTLCartUnix.tar.Z % tar xf QTLCartUnix.tar See the file doc/txt/INSTALL on how to install the programs. Adobe PDF files containing the documentation are also in the doc/pdf subdirectory. **** For Macintosh: PowerMac binaries are in the file QTLCartMac.sea.hqx. You will need to unbinhex the download and then double click the self-extracting binary. The folder 'bin' has the PowerMac binaries. The folder 'cbin' has the Carbon binaries for use with MacOS X. The 'doc' and 'example' folders have documentation and example files. **** Notes: Remember that the programs all act like Unix programs, and you can get a list of command line options by invoking the program with the argument -h. An example: brooks:~ % Rmap -h ====================================================================== QTL Cartographer v. 1.14d, 3/31/2000 Copyright (C) 1996-1999 C. J. Basten, B. S. Weir and Z.-B. Zeng. QTL Cartographer comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. For details select help. ====================================================================== TIME: 14:19:11 on Wednesday, 21 June 2000 PROGRAM: Rmap PURPOSE: Create or translate a genetic linkage map USAGE: Rmap [-i x] [-o x] [-e x] ... DEFAULTS: [ -i ] Input File [ -o qtlcart.map ] Output File [ -e qtlcart.log ] Error File [ -s 961611551 ] Random Number Seed [ -f 1 ] Map Function [1,8], 1 => Haldane [ -p 0.000000 ] Map Function Parameter [ -g 1 ] Ouput (1,2,3) => Text, Graphics, Both [ -c 4 ] Chromosomes [ -m 16 ] Markers per Chromosome [-vm 0.000000 ] Standard Deviation of Markers per Chromosome [ -d 10.000000 ] Intermarker Distance (cM) [-vd 0.000000 ] Standard Deviation of Intermarker Distance (cM) [ -t 0.000000 ] Tails (Flanking DNA, in cM) [ -M 0 ] Simulation Mode (0,1) Also: [-h] for help, [-A] for automatic, [-V] for non-Verbose [-W path] for a working directory, [-R file] to specify a resource file and [-X stem] to specify a filename stem. ====================================================================== Now exiting program without doing any calculations. You may need to click on the upper right X to close this screen ====================================================================== The manual gives a better explanation of the options. A PDF version is in the manual.pdf file in the doc/pdf subdirectory. Also, the file qtlcart.hlp provides online help. **Please join the mailing list for QTL Cartographer. It will be a forum for problems you may have in using the programs, and we will post announcements of updates and bug fixes. To subscribe, send the following one line message to MajorDomo@statgen.ncsu.edu: subscribe qtlcart **Send any bug reports to qtlcart-bug@statgen.ncsu.edu. ***************************************************************** Chris Basten B. S. Weir Zhao-Bang Zeng Email: basten@statgen.ncsu.edu zeng@statgen.ncsu.edu Phone: (919)515-1934 (919)515-1942 Fax: (919)515-7315 Address: Department of Statistics North Carolina State University Raleigh, NC 27695-8203 USA ***************************************************************** ÿ