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Table of Contents
REMLF90
Variance component estimation program with EM-REML algorithm.
Summary
Options
OPTION conv_crit1d-12
Convergence criterion (default 1d-10).
OPTION maxrounds500
Maximum rounds (default 5000).
OPTION constant_var 5 1 2
5: effect number 1: first trait number 2: and the second trait number implying the covariance between traits 1 and 2 for effect 5.
OPTION SNP_file snp
Specify the SNP file name to use genotype data.
Does remlf90 always converge?
Even when there is no variance, remlf90 will estimate a positive variance (in the parameter space), which will be determined by the starting value. If you are not sure if there is any variance, use a small starting value like 0.1 or 0.01. If the estimate does not change, probably there is no variance, so check your parameter file, model, and/or data again. If airemlf90 does not converge but remlf90 converges with the same dataset, rerun remlf90 with a small starting value. The estimate could be artifact.