readme.pcg2
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| readme.pcg2 [2012/05/29 17:04] – shogo | readme.pcg2 [2013/07/17 16:20] – shogo | ||
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| \\ | \\ | ||
| The original program was written by Shogo Tsuruta in 1999. | The original program was written by Shogo Tsuruta in 1999. | ||
| + | See PREGSF90 with genotypes (SNP) for options. | ||
| ===== Summary===== | ===== Summary===== | ||
| - | BLUP90IOD2 is a BLUP program for solving a large number of mixed model equations, using preconditioned conjugate gradient (PCG). | + | 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. |
| ====== Options ====== | ====== Options ====== | ||
| Line 22: | Line 23: | ||
| 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 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 solutions | + | To restart the program from the previous solutions. |
| < | < | ||
| OPTION missing -1 | OPTION missing -1 | ||
| Line 34: | Line 51: | ||
| 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 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. " | ||
| < | < | ||
| OPTION SNP_file snps | OPTION SNP_file snps | ||
| </ | </ | ||
| - | implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse) | + | implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse). |
| //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.// | ||
readme.pcg2.txt · Last modified: 2024/05/16 14:16 by dani