The original program was written by Shogo Tsuruta in 1999.
BLUP90IOD2 is a BLUP program for solving a large number of mixed model equations, using preconditioned conjugate gradient (PCG). Another version for heterogeneous residual variances is also available.
See PREGSF90 with genotypes (SNP) for options.
Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse).

OPTION conv_crit 1e-12

Set a convergence criterion (default 1e-12). Usually, a stricter criterion (e.g., 1e-14 to 1e-16) is needed with a single-trait model than a multiple-start model.

OPTION maxrounds 10000

Set maximum number of rounds (default 5000).

OPTION blksize 3

Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, the number can be the number of traits.

OPTION init_eq 10

Set the number of effects to be solved directly (default=0) to accelerate convergence (usually, 10% to 50% faster).

OPTION solv_method FSPAK

Solving method for initial equations (default=DIRECT).

OPTION tol 1d-12

Tolerance to get a positive definite covariance component matrix (default=1d-12).

OPTION residual

y-hat and residuals will be included in “yhat_residual”.

OPTION avgeps 50

Using the last 50 average eps for convergence, depending on the fluctuation of convergence. When using this option, the convergence criterion can be loosen (e.g., 1e-12 → 1e-10, 1e-14 → 1e-12), also depending on how convergence fluctuates.

OPTION cont 1

To restart the program from the previous solutions.

OPTION missing -999

Set the missing value (default 0) in integer.

OPTION restart 100

Set the number of iteration to recompute residuals (default=100).

OPTION prior_solutions

Using the previous solution file to start the iteration. An additional software is required to use this option.

OPTION random_upg 1 2

Set the UPG random. “1” the weight for random UPG = 1. If the second number exits, the weight will be inverted (e.g., 1/2=0.5).

OPTION SNP_file snp

Specify the SNP file name to use genotype data.
For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.