readme.pcg2
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readme.pcg2 [2012/05/29 16:02] – shogo | readme.pcg2 [2020/01/23 00:26] – [Options] shogo | ||
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- | ====== BLUP90IOD2====== | + | ====== BLUP90IOD2 ====== |
- | \\ | + | |
- | The original program was written by Shogo Tsuruta in 1999. | + | |
- | ===== Summary===== | + | ===== Summary ===== |
- | BLUP90IOD2 is a BLUP program for solving a large number of mixed model equations, using preconditioned conjugate gradient (PCG). | + | 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). | ||
====== Options ====== | ====== Options ====== | ||
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OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
</ | </ | ||
- | set convergence | + | Set a convergence |
< | < | ||
OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
</ | </ | ||
- | set maximum number of rounds (default | + | Set maximum number of rounds (default |
< | < | ||
OPTION blksize 3 | OPTION blksize 3 | ||
</ | </ | ||
- | set block size for preconditioner (default 1). | + | 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 | OPTION init_eq 10 | ||
</ | </ | ||
- | set the number of effects to be solved directly (default=0) | + | Set the number of effects to be solved directly (default=0) |
+ | < | ||
+ | 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 " | ||
+ | < | ||
+ | OPTION avgeps 50 | ||
+ | </ | ||
+ | Using the last 50 average eps for convergence, | ||
< | < | ||
OPTION cont 1 | OPTION cont 1 | ||
</ | </ | ||
- | to restart the program from the previous | + | To restart the program from the last solutions. |
< | < | ||
- | OPTION missing -1 | + | OPTION missing -999 |
</ | </ | ||
- | set the missing value (default 0). | + | Set the missing value (default 0) in integer. |
< | < | ||
OPTION restart 100 | OPTION restart 100 | ||
</ | </ | ||
- | set the number of iteration to recompute residuals (default=100) | + | Set the number of iteration to recompute residuals (default=100). |
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
- | implement one-step genomic selection updating animal effects with genomic relationship matrix | + | 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. " | ||
+ | < | ||
+ | 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.// | //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.// | ||
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readme.pcg2.txt · Last modified: 2024/05/16 14:16 by dani