SIMER

<img alt="Hits" src="https://hits.sh/github.com/xiaolei-lab/SIMER.svg?view=today-total&label=Today%2FTotal%20Visitors&extraCount=12000"/>

Data Simulation for Life Science and Breeding

Authors:

Design and Maintenance: Dong Yin, Xuanning Zhang, Lilin Yin ,Haohao Zhang, and Xiaolei Liu.
Contributors: Zhenshuang Tang, Jingya Xu, Xiaohui Yuan, Xiang Zhou, Xinyun Li, and Shuhong Zhao.
Citation: Yin D., Zhang X, Yin L, Zhang H, Tang Z, Xu J, Yuan X, Zhou X, Li X, Zhao S, Liu X. SIMER: an accurate and intelligent tool for simulating customizable population data across species in complex scenarios, Journal of Big Data , 2025, 12 (49), doi: https://doi.org/10.1186/s40537-025-01102-z.

If you have any bug reports or questions, please feed back :point_right:here:point_left:.

:toolbox: Relevant software tools for genetic analyses and genomic breeding

<table> <tr> <td><g-emoji class="g-emoji" alias="mailbox" fallback-src="https://github.githubassets.com/images/icons/emoji/unicode/1f4eb.png">📫</g-emoji> <strong><a href="https://www.hiblup.com/" rel="nofollow">HIBLUP</a></strong>: Versatile and easy-to-use GS toolbox.</td> <td><g-emoji class="g-emoji" alias="mountain_snow" fallback-src="https://github.githubassets.com/images/icons/emoji/unicode/1f3d4.png">🏔️</g-emoji> <strong><a href="https://ianimal.pro/" rel="nofollow">IAnimal</a></strong>: an omics knowledgebase for animals.</td> </tr> <tr> <td><g-emoji class="g-emoji" alias="biking_man" fallback-src="https://github.githubassets.com/images/icons/emoji/unicode/1f6b4-2642.png">🚴&zwj;♂️</g-emoji> <strong><a href="https://github.com/YinLiLin/KAML">KAML</a></strong>: Advanced GS method for complex traits.</td> <td><g-emoji class="g-emoji" alias="bar_chart" fallback-src="https://github.githubassets.com/images/icons/emoji/unicode/1f4ca.png">📊</g-emoji> <strong><a href="https://github.com/YinLiLin/CMplot">CMplot</a></strong>: A drawing tool for genetic analyses.</td> </tr> <tr> <td><g-emoji class="g-emoji" alias="postbox" fallback-src="https://github.githubassets.com/images/icons/emoji/unicode/1f4ee.png">📮</g-emoji> <strong><a href="https://github.com/xiaolei-lab/rMVP">rMVP</a></strong>: Efficient and easy-to-use GWAS tool.</td> <td><g-emoji class="g-emoji" alias="swimmer" fallback-src="https://github.githubassets.com/images/icons/emoji/unicode/1f3ca.png">🏊</g-emoji> <strong><a href="https://github.com/YinLiLin/hibayes">hibayes</a></strong>: A Bayesian-based GWAS and GS tool.</td> </tr> </table>

Contents

<!-- TOC updateOnSave:false -->

• Installation
• Data Preparation
  • Genotype
  • Genetic map
  • Pedigree<img src="https://raw.githubusercontent.com/xiaolei-lab/SIMER/master/inst/extdata/00simer_logo/simer_logo.png" height="250" align="right" />
• Data Input
  • Basic
  • Optional
• Quick Start
  • Quick Start for Population Simulation
  • Quick Start for Genotype Simulation
  • Quick Start for Phenotype Simulation
• Genotype Simulation
  • Gallery of genotype simulation parameters
  • Generate an external or species-specific or random genetic map
  • Generate an external or species-specific or random genotype matrix
  • Generate a genotype matrix with complete linkage disequilibrium
  • Add chromosome crossovers and mutations to genotype matrix
• Phenotype Simulation
  • Gallery of phenotype simulation parameters
  • Generate phenotype using an external or species-specific or random genotype matrix
  • Generate continuous phenotype
  • Generate case-control phenotype
  • Generate categorical phenotype
  • Generate phenotype using A model
  • Generate phenotype using AD model
  • Generate phenotype using GxG model
  • Generate phenotype using Repeated Record model
  • Generate phenotype controlled by QTNs subject to Normal distribution
  • Generate phenotype controlled by QTNs subject to Geometric distribution
  • Generate phenotype controlled by QTNs subject to Gamma distribution
  • Generate phenotype controlled by QTNs subject to Beta distribution
  • Generate phenotype with fixed effect and covariate and environmental random effect
  • Generate phenotype using GxE model
  • Generate phenotype using ExE model
  • Generate phenotype controlled by varied QTN effect distribution
• Population Simulation of Multiple-Generation with Genotype and Phenotype
  • Gallery of population simulation parameters
  • Individual selection for a single trait
  • Family selection for a single trait
  • Within-family selection for a single trait
  • Combined selection for a single trait
  • Tandem selection for multiple traits
  • Independent culling selection for multiple traits
  • Index selection for multiple traits
  • Clone for plants
  • Doubled haploid for plants
  • Self-pollination for plants and micro-organisms
  • Random mating for plants and animals
  • Random mating excluding self-pollination for animals
  • Assortative mating for plants and animals
  • Disassortative mating for plants and animals
  • Two way cross for animals
  • Three way cross for animals
  • Four way cross for animals
  • Back cross for animals
  • User-designed pedigree mating for plants and animals
  • AN EASY WAY TO GENERATE A POPULATION
• Breeding Program Design
  • Gallery of breeding program design parameters
  • Definition of a breeding program design
  • Data quality control
  • Model optimization
  • Construction of selection index
• Global Options
  • Gallery of global parameters
  • Counts of total population size
  • Multi-thread computation
  • Multi-population simulation
  • File output
  • Generation-selective output
• Output
  • Annotation data
  • Genotype data
  • Phenotype data
• Citation
• FAQ and Hints

<!-- /TOC -->

---

Installation

back to top

WE STRONGLY RECOMMEND TO INSTALL SIMER ON Microsoft R Open (https://mran.microsoft.com/download/).

Installation

• The stable version:

install.packages("simer")

• The latest version:

devtools::install_github("xiaolei-lab/SIMER")

After installed successfully, SIMER can be loaded by typing

> library(simer)

Typing ?simer could g