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CLC number: Q78; TP31

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Received: 2007-09-12

Revision Accepted: 2007-09-14

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Journal of Zhejiang University SCIENCE B 2007 Vol.8 No.11 P.815-821

http://doi.org/10.1631/jzus.2007.B0815


WOMBAT—A tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML)


Author(s):  MEYER Karin

Affiliation(s):  Animal Genetics and Breeding Unit, University of New England, Armidale, New South Wales 2351, Australia

Corresponding email(s):   kmeyer@didgeridoo.une.edu.au

Key Words:  Software, Variance components, Genetic parameters, Mixed model, Restricted maximum likelihood


MEYER Karin. WOMBAT—A tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML)[J]. Journal of Zhejiang University Science B, 2007, 8(11): 815-821.

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Abstract: 
WOMBAT is a software package for quantitative genetic analyses of continuous traits, fitting a linear, mixed model; estimates of covariance components and the resulting genetic parameters are obtained by restricted maximum likelihood. A wide range of models, comprising numerous traits, multiple fixed and random effects, selected genetic covariance structures, random regression models and reduced rank estimation are accommodated. WOMBAT employs up-to-date numerical and computational methods. Together with the use of efficient compilers, this generates fast executable programs, suitable for large scale analyses. Use of WOMBAT is illustrated for a bivariate analysis. The package consists of the executable program, available for LINUX and WINDOWS environments, manual and a set of worked example, and can be downloaded free of charge from http://agbu.une.edu.au/~kmeyer/wombat.html

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

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[3] Karypis, G., Kumar, V., 1998. METIS, a Software Package for Partitioning Unstructured Graphs, Partitioning Meshes, and Computing Fill-in Reducing Ordering of Sparse Matrices Version 4.0. Department of Computer Science, University of Minnesota, Minneapolis, p.44.

[4] Kovacs, M.A., Groeneveld, E., 2003. VCE-5 User’s Guide and Reference Manual, Version 5.1. Institute of Animal Husbandry and Animal Behaviour, Federal Research Center of Agriculture, Mariensee, Germany, p.68.

[5] Liu, C., Rubin, D.B., Wu, Y.N., 1998. Parameter expansions to accelerate EM: the PX-EM algorithm. Biometrika, 85(4):755-770.

[6] Madsen, P., Jensen, J., 2006. A User’s Guide to DMU: A Package for Analyzing Multivariate Mixed Models, Version 6. Danish Institute of Agricultural Sciences, Dept. of Animal Breeding and Genetics, Research Centre Foulum, 8830 Tjele, Denmark, p.27.

[7] Mäntysaari, E.A., 1999. Derivation of Multiple Trait Reduced Random Regression (RR) Model for the First Lactation Test Day Records of Milk, Protein and Fat. In: 50th Annual Meeting. Europ. Ass. Anim. Prod. Mimeo, p.8.

[8] Meyer, K., 1988. DFREML—a set of programs to estimate variance components under an individual animal model. J. Dairy Sci., 71(Suppl. 2):33-34.

[9] Meyer, K., 1991. Estimating variances and covariances for multivariate animal models by restricted maximum likelihood. Genet. Sel. Evol., 23(1):67-83.

[10] Meyer, K., 2005a. Ordering strategies to reduce computational requirements in variance component estimation. Proc. Ass. Advan. Anim. Breed. Genet., 16:282-285.

[11] Meyer, K., 2005b. Genetic principal components for live ultra-sound scan traits of Angus cattle. Anim. Sci., 81(3):337-345.

[12] Meyer, K., 2007. Multivariate analyses of carcass traits for Angus cattle fitting reduced rank and factor-analytic models. J. Anim. Breed. Genet., 124(2):50-64.

[13] Misztal, I., Perez-Encisco, M., 1993. Sparse matrix inversion for restricted maximum likelihood estimation of variance components by Expectation-Maximization. J. Dairy Sci., 76(5):1479-1483.

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Open peer comments: Debate/Discuss/Question/Opinion

<1>

SORAYA@RAFIEE<SORAYA.RAFIEE@YAHOO.COM>

2014-08-17 12:09:20

Hi;
I hope you are good.
I really enjoy wombat software
but I can't provide parameter file for using random regression models.
I need to see examples with more details about especially data set.
please help me.
thanks for your efforts.

liushudong@xinjaing sheep center<liushudong63@126.com>

2014-08-07 12:42:39

hello,we will learn sofeware tool.

Please provide your name, email address and a comment





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