PyPedal: A computer program for pedigree analysis

Computers and Electronics in Agriculture

Volumn 57, Issue 1, 2007, Pages 107-113

  Cole, John B ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Inbreeding; Pedigree analysis; Pedigree simulation; Visualization

Indexed keywords

COMPUTER PROGRAMMING LANGUAGES; COMPUTER SIMULATION; GENES; GRAPH THEORY; NUMERICAL ANALYSIS; VISUALIZATION;

INBREEDING; MICROSOFT WINDOWS; PEDIGREE ANALYSIS; PEDIGREE SIMULATION;

ERROR CORRECTION;

ANCESTRY; GENETIC VARIATION; INBREEDING; NUMERICAL METHOD; SOFTWARE;

BOS; CANIS FAMILIARIS;

EID: 33947730498     PISSN: 01681699     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compag.2007.02.002     Document Type: Article

References (19)

1. Boichard D. PEDIG: a FORTRAN package for pedigree analysis suited for large populations. Comm. 28-13 in Proceedings of the 7th World Congr. Genet. Appl. Livest. Prod. Montpellier, France (2002)
2. Boichard D., Maignel L., and Verrier E. The value of using probabilities of gene origin to measure genetic variability in a population. Genet. Select. Evol. 29 (1997) 5-23
3. Cassell B.G., Adamec V., and Pearson R.E. Effect of incomplete pedigrees on estimates of inbreeding and inbreeding depression for days to first service and summit milk yield in Holsteins and Jerseys. J. Dairy Sci. 86 (2003) 2967-2976
4. Cole J.B., and Franke D.E. Pedigree analysis using the Python programming language. J. Anim. Sci. 80 Suppl. 1 (2002) 323 (abstract)
5. Cole J.B., Franke D.E., and Leighton E.A. Population structure of a colony of dog guides. J. Anim. Sci. 82 (2004) 2906-2912
6. Cormen T.H., Leiserson C.E., Rivest R.L., and Stein C. Introduction to Algorithms. 2nd ed. (2003), Prentice-Hall, New York
7. Emik L.O., and Terrill C.E. Systematic procedures for calculating inbreeding coefficients. J. Heredity 40 (1949) 51-55
8. Falconer D.S., and MacKay T.F. Introduction to Quantitative Genetics. 4th ed. (1996), John Wiley & Sons Inc., New York
9. Gansner E.R., and North S.C. An open graph visualization system and its applications to software engineering. Softw. Pract. Exp. 00 S1 (1999) 1-5
10. Gutiérrez J.P., and Goyache F. A note on ENDOG: a computer program for analyzing pedigree information. J. Anim. Breed. Genet. 122 (2005) 172-176
11. Henderson C.R. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32 (1976) 69-83
12. Huang Y.C., and Shanks R.D. Visualization of inheritance patterns from graphic representation of additive and dominance relationships between animals. J. Dairy Sci. 78 (1995) 2877-2883
13. Lacy R.C. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol. 8 (1989) 111-123
14. MacCluer J.W., VandeBerg J.L., Read B., and Ryder O.A. Pedigree analysis by computer simulation. Zoo Biol. 5 (1986) 147-160
15. Newman M.E.J. The structure and function of complex networks. SIAM Rev. 45 (2003) 167-256
16. Quaas R.L. Computing the diagonal elements of a large numerator relationship matrix. Biometrics 32 (1976) 949-953
17. Sargolzaei M., Iwaisaki H., and Colleau J.J. CFC: a tool for monitoring genetic diversity. Comm 27-28 in Proceedings of the 8th World Congr. Genet. Appl. Livest. Prod. Belo Horizonte, Brazil (2006)
18. VanRaden P.M. Accounting for inbreeding and crossbreeding in genetic evaluation of large populations. J. Dairy Sci. 75 (1992) 3136-3144
19. Wright S. Coefficients of inbreeding and relationship. Am. Nat. 56 (1922) 330-338