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start [2012/05/10 19:48] – ignacy | start [2014/04/25 13:18] – [BLUPF90 Family of Programs] andres | ||
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=== now with support for genomic selection === | === now with support for genomic selection === | ||
- | //Ignacy Misztal and collaborators, | + | //Ignacy Misztal and collaborators, |
- | BLUPF90 family of programs is a collection of software in Fortran 90/95 for mixed model computations in animal breeding. The goal of the software is to be as simple as with a matrix package and as efficient as in a programming language. | + | |
+ | BLUPF90 family of programs is a collection of software in Fortran 90/95 for mixed model computations in animal breeding. The goal of the software is to be as simple as with a matrix package and as efficient as in a programming language. | ||
- | For variance component estimation, the family offers choices for simple and complicated models; see paper “Reliable computing in estimation of variance components”. From 2009 the programs are successively modified for genomic selection using a single-step approach (or ssGBLUP) by Ignacio Aguilar and Shogo Tsuruta. | + | For variance component estimation, the family offers choices for simple and complicated models; see paper {{reliable_computing.pdf| |
====== Headline ====== | ====== Headline ====== | ||
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* [[Support]] | * [[Support]] | ||
* [[FAQ]] | * [[FAQ]] | ||
+ | * [[Tricks]] | ||
+ | * [[Course materials - from UGA 2012]] | ||
+ | |||
- | FAQ for BLUPF90 programs | ||
- | Input files | ||
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- | data | ||
- | pedigree | ||
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- | Data preparation program | ||
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- | renumf90 (ver 1.92) read me | ||
- | examples | ||
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- | Frequent mistakes in a parameter file for BLUPF90 programs | ||
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- | parameter files for various models | ||
- | examples | ||
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- | REML | ||
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- | remlf90 (ver 1.76) read me: EM algorithm - PDF | ||
- | airemlf90 (ver 1.99) read me: Average Information REML + REMLF90 - Standard Errors (PDF) | ||
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- | Gibbs sampling | ||
- | OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed variances | ||
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- | gibbs1f90 (ver 1.42) read me: Faster than GIBBS2F90 without missing traits | ||
- | gibbs2f90 (ver 1.76) read me | ||
- | gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances | ||
- | thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model | ||
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- | Post-Gibbs Analysis | ||
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- | postgibbsf90 (ver 3.02) read me: Needs Gibbs samples and gnuplot (use postgibbsold for old Gibbs sampler programs) | ||
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- | BLUP | ||
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- | blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF | ||
- | blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions) | ||
- | cblup90iod2 (ver 3.16) read me: Threshold model + linear model for a large number of equations (available only under some conditions) | ||
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- | Accuracy | ||
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- | accf90 : (ver 1.63) read me: Accuracy (reliability) for a large number of animals (available only under some conditions) | ||
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- | Genomic Analysis | ||
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- | preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs |
start.txt · Last modified: 2024/04/04 13:54 by dani