DHSMAP (Decay of Haplotype Sharing MAPping software) A program that fine-maps qualitative traits by linkage disequilibrium. Copyright (C) 2000 Andrew Strahs, Kenneth Wilder, Mary Sara McPeek Homepage: http://galton.uchicago.edu/~mcpeek/software/dhsmap Release 2.0 October 18, 2001 =========================================================== License This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY of FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program (see file gpl.txt); if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. We request that use of this software be cited in publications as McPeek MS, Strahs AL (1999) Assessment of Linkage Disequilibrium by the Decay of Haplotype Sharing, with Application to Fine-Scale Genetic Mapping. Am J Hum Genet 65:858-875 To contact the author: Andrew Strahs Department of Biostatistics Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115 email: astrahs@hsph.harvard.edu =========================================================== Installation instructions: 1. Download the DHSMAP package. This package contains documentation, source code, and precompiled executables for Linux and Solaris platforms. 2. Read the sections "Overview" (overview.txt), "Search Procedures" (searchproc.txt), "Input" (input.txt), "Output" (output.txt) and "Tips" (tips.txt) carefully to understand the purpose of this program and how it works. 3. Edit Makefile as necessary according to the instructions in Makefile. You should only need to make sure that the correct compiler and compiler options for your machine are chosen. 4. Type "make". This will build an executable program "dhsmap". 5. To run the executable program dhsmap: First, prepare the input files, e.g., datafile_ex and pedfile_ex (see "Input" for more details). Then, type dhsmap datafile_ex pedfile_ex (Note: Replace names of example input files with those that contain your data) 6. You can test the executable program dhsmap by running it with the sample input files datafile_ex and pedfile_ex. You can then compare your output in the files "resout", "ancout", "maxout", and "oneout" with the correct output in the sample output files "resout_ex", "ancout_ex", "maxout_ex", and "oneout_ex". (Note: On our Linux PC [PIII-500 processor], this example takes 4 minutes, 34 seconds; on our Sun Ultra 2 Workstation, the running time is 8 minutes, 10 seconds.) 7. The program stops if any errors are detected in the format of the input files or if any errors appear while the software is running. Check the file "dhsmap_errors" for all the errors.