Home

• 1 Introduction
• 2 Manual
  • general
  • input data
  • output
• 3 Walkthrough
  • basic introduction: Simulations of diploids using toy-examples
  • simulations of haploids and clonal evolution
  • simulations of diploids using realistic data-sets
  • generating input files for MimicrEE2
  • visualization of the output
  • misc
• 4 Validation
• 5 Cite

1 Introduction

MimicrEE2 allows performing genome-wide forward simulations for Evolve and Resequencing studies. Simulations may be performed for populations of diploid or haploid organisms using a realistic genomic context. This enables to use available genomic resources for a species of interest such as recombination rate estimates, sequenced haplotypes, known causative loci etc. MimicrEE2 supports a classic model of selection with loci having a constant selection coefficient as well as a quantitative model. This allows simulating many different adaptive scenarios such as loci with constant selection coefficients, complex epistasis, truncating selection, stabilizing selection, disruptive selection, diminishing returns epistasis, adaptation to a moving optimum. As output a summary of the allele frequencies, the haplotypes or the fitness/phenotype of the individuals, may be provided. We also demonstrate how to generate Manhattan plots, how to compare the performance of different approaches with ROC curves and how to run MimicrEE2 on a computer cluster using Apache Spark.

2 Manual

general

• [FeaturesAndDifferences] Potential use cases, full list of features and differences between MimcrEE1 and MimicrEE2.
• [Manual]
• [ReleaseNotes]
• License: GPLv3 https://www.gnu.org/licenses/gpl-3.0.de.html

input data

• [HaplotypeFile] the haplotypes of the not evolved base population
• [RecombinationRate] the recombination rate
• [sex] specify the sexes, the sex ratio and the hemizygous sex chromosomes
• [SelectedLoci] effect sizes and selection coefficients of selected loci
• [SelectionRegimes] fitness functions and truncating selection (modes qt and qff)
• [MiscInput] chromosome definition, population size, and migration regime

output

• [OutputFiles]

3 Walkthrough

basic introduction: Simulations of diploids using toy-examples

• [MinimalWalkthrough] introduction to simulations with MimicrEE2 using a toy example (w-mode)
• [MinimalWalkthroughWithSex] a toy example demonstrating simulations of different sexes (w-mode)
• [MinimalWalthroughWithSexChromosome] a toy example showing simulation of a hemizygous sex chromosomes (w-mode)
• [MutationWalkthrough] a toy example demonstrating simulations with mutations (w-mode)
• [MigrationWalkthrough] a toy example demonstrating simulations with migration (w-mode)

simulations of haploids and clonal evolution

• [HaploidSimulations] introduction to simulations of haploid organisms using toy examples (w-mode)
• [ClonalEvolution] simulations of clonal evolution using toy examples (w-mode)
• [Example of microbial evolution]

simulations of diploids using realistic data-sets

• [Walkthrough for w mode] simulations with a large data set: selected loci, epistatic interactions and neutral simulations
• [Walkthrough for qt mode] simulations with a large data set: truncating selection of a quantitative trait
• [Walkthrough for qff mode] simulations with a large data set: stabilizing selection and adaptation to a moving optimum for a quantitative trait

generating input files for MimicrEE2

• [GeneratingSimpleHaplotypes] generate simple haplotypes
• [GeneratingHaplotypesWithFastsimcoal] simulate complex haplotypes with fastsimcoal and convert the output to MimicrEE2 haplotypes
• [UsingExistingHaplotypesEgDGRP] convert sequenced haplotypes from Drosophila (vcf file) to MimicrEE2 haplotypes
• [GeneratingSimpleRecombinationMap] generate a simple recombination map
• [UsingAnExistingRecombinationMap] convert the recombination map from Drosophila to a file format comptabile with MimicrEE2
• [RandomSNPsWMode] randomly pick selected SNPs for the w-mode
• [RandomSNPsQTL] randomly pick QTLs for the qt-mode or qff-mode

visualization of the output

• [How to make Manhattan plots with MimicrEE2]
• [How to make ROC curves with MimicrEE2]

misc

• [Mimhap2Fasta] a toy example demonstrating the conversion of MimicrEE2 haplotypes into fasta entries
• [BioExample] Biological example: simulating adaptation to starvation conditions
• [Run MimicrEE2 on a cluster]

4 Validation

• [DriftDistribution]
• [ResponsetoSelection]
• [SelectionCoefficient]
• [LinkageDisequilibrium]
• [Migration]
• [RecombinationFraction]
• [MatingFunctions]
• [MutationGenerator]

5 Cite

Christos Vlachos and Robert Kofler (2018): MimicrEE2: Genome-wide forward simulations for Evolve and Resequencing studies; PLoS Comput Biol. 2018 Aug 16;14(8):e1006413.
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006413

Project Members:

• Christos Vlachos (admin)
• Robert Kofler (admin)