ArticleGenetics, selection, evolution : GSE2020
SeqBreed: a python tool to evaluate genomic prediction in complex scenarios.
Article in Genetics, selection, evolution : GSE, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Bridging tradition and innovation: a review of computer simulations in plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- A guide to plant breeding for animal breeders.G3 (Bethesda, Md.) · 2026Review
- ADAM-multi: software to simulate complex breeding programs for animals and plants with different ploidy levels and generalized genotypic effect models to account for multiple alleles.Frontiers in genetics · 2025Article
- Computational tools for plant genomics and breeding.Science China. Life sciences · 2024Review
- Simulation of functional additive and non-additive genetic effects using statistical estimates from quantitative genetic models.Heredity · 2024Article
- Quantitative evaluation of nonlinear methods for population structure visualization and inference.G3 (Bethesda, Md.) · 2022Article
- MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms.Ecology and evolution · 2021Article
- MoBPSweb: A web-based framework to simulate and compare breeding programs.G3 (Bethesda, Md.) · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundGenomic prediction (GP) is a method whereby DNA polymorphism information is used to predict breeding values for complex traits. Although GP can significantly enhance predictive accuracy, it can be expensive and difficult to implement. To help design optimum breeding programs and experiments, including genome-wide association studies and genomic selection experiments, we have developed SeqBreed, a generic and flexible forward simulator programmed in python3.
resultsSeqBreed accommodates sex and mitochondrion chromosomes as well as autopolyploidy. It can simulate any number of complex phenotypes that are determined by any number of causal loci. SeqBreed implements several GP methods, including genomic best linear unbiased prediction (GBLUP), single-step GBLUP, pedigree-based BLUP, and mass selection. We illustrate its functionality with Drosophila genome reference panel (DGRP) sequence data and with tetraploid potato genotype data.
conclusionsSeqBreed is a flexible and easy to use tool that can be used to optimize GP or genome-wide association studies. It incorporates some of the most popular GP methods and includes several visualization tools. Code is open and can be freely modified. Software, documentation, and examples are available at https://github.com/miguelperezenciso/SeqBreed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.