USER MANUAL VERSION 2.1

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1 A computer program for minimizing inbreeding coefficients in breeding plans USER MANUAL VERSION 2.1 JOHN R. GARBE 1 AND YANG DA 2 1 MINNESOTA SUPERCOMPUTER INSTITUTE 2 DEPARTMENT OF ANIMAL SCIENCE UNIVERSITY OF MINNESOTA NOVEMBER

2 1 INTRODUCTION OPERATION GETTING STARTED: On Microsoft Windows: On Unix INPUT FILES DATA FILE BREEDER FILE PARAMETER FILE Options OUTPUT REFERENCES

3 1 Introduction MiniInbred predicts inbreeding levels in the next generation by identifying matings that yield the lowest inbreeding level in the offspring. The inbreeding coefficients resulting from all potential matings of the current breeding animals (generation 1) are calculated, and the potential matings among the current breeding animals that yield the lowest inbreeding level are identified. The program also has the option to predict the lowest inbreeding available in the third generation. In this case, the hypothetical offspring (generation 2) of the current breeding animals are treated as 'parents', and the inbreeding coefficients resulting from all potential matings between the hypothetical 'parents' are calculated, and the potential matins among the hypothetical 'parents' that minimize inbreeding are identified. 2 Operation 2.1 Getting Started: MiniInbred current is available for Linux and Windows operation systems. The executable files can be down loaded at The computer systems and the corresponding downloadable files are listed below: Operation system Linux Windows Downloadable file MiniInbred_2.0_Linux.tar.gz MiniInbred_2.0_Windows.zip On Microsoft Windows: To run MiniInbred on Windows, open an MS/DOS window and move to the directory where the MiniInbred executable is located. Create or edit the miniinbred.dat parameter file if needed. The parameter file specifies the program options. Type MiniInbred.exe followed by the name of the input file to run the program. Diagnostic information and program output will be printed to the screen. Alternatively, simply double-click the MiniInbred.exe file, and type in the name of the input file at the prompt On Linux To run MiniInbred on Linux, open a Linux terminal and move to the directory where the MiniInbred executable is located. Create or edit the miniinbred.dat parameter file if needed. The parameter file specifies the program options. Type miniinbred followed by the name of the input file to run the program. Diagnostic information and program output will be printed to the screen. NOTE: before running MiniInbred for the first time on Linux you may need to change the permissions on the executable with this command: $chmod u+x miniinbred 3

4 3 Input Files MiniInbred uses three input files, a data file containing pedigree information, a breeder file containing a list of breeding individuals, and a parameter file containing program options. 3.1 Data File The data file is a simple text file that contains the pedigree information for a population. Each line of the file gives the ID of an individual as well as the IDs of the individual s parents and the gender of the individual. A parental ID of 0 indicates an unknown individual. A sample input file is shown below. Sample input file Sire 0 0 M Dam 0 0 F Offspring1 Sire Dam M Offspring2 Sire Dam M Offspring3 Sire Dam M Offspring4 Sire Dam M Offspring5 Sire Dam F Offspring6 Sire Dam F Offspring7 Sire Dam F Offspring8 Sire Dam F The datafile must contain 4 columns of data for each individual. The datafile is specified on the command line. 3.2 Breeder File The breeder file contains the list if individual s IDs to be considered as the first generation. 3.3 Parameter File MiniInbred program options are specified in a simple text parameter file named miniinbred.dat. One option should be listed per line. Lines beginning with # are ignored, as are blank lines. 4

5 3.3.1 Options Option Name Default Value Description male M A string that indicates a male individual female F A string that indicates a female individual verbose Print progress information to the screen while the program is running breederfile The name of the file containing the list of breeding individuals outputfile Name of the output file. If an output file is not specified the program output will be printed to the screen. secondgen The number of individuals in the second generation thirdgen The number of individuals in the third generation 4 Output Mininbred prints out the inbreeding coefficients for all individuals in generation 1 and the individuals with lowest inbreeding coefficients in generations 2 and 3. The average inbreeding coefficients for each generation are computed and displayed as well. 5 References Garbe, J. R. and Y. Da (2014) MiniInbred: A computer program for minimizing inbreeding coefficients in breeding plans. User Manual Version 2.1. Department of Animal Science, University of Minnesota. Acknowlegements MiniInbred version 2.1 was supported by USDA National Institute of Food and Agriculture Grant no and by project MN of the Agricultural Experiment Station at the University of Minnesota, and MiniInbred versions 1.1 and 2.0 were supported by Cargill, Inc. 5

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