Secondary_E&R_Sim Files

#Anna Maria Langmüller
#Vetmeduni Vienna
#05/2021
#Secondary E&R Sim
#README: mimicree-input-files 

1to1_300/Florida_[id]-Florida_[id]-N300-p050-simB.modified.sex.tab.tar.gz
	input files, crossing scheme=1:1, N=300 individuals 
	four different mixtures of focal/non-focal lines 
	20 input files in total 

1to1_1200/Florida_[id]-Florida_[id]-N1200-p050-simB.modified.sex.tab.tar.gz
	input files, crossing scheme=1:1, N=1200 individuals
	four different mixtures of focal/non-focal lines 
	20 input files in total 

1to1_4800/Florida_[id]-Florida_[id]-N4800-p050-simB.modified.sex.tab.gz
	input files, crossing scheme=1:1, N=4800 individuals
	four different mixtures of focal/non-focal lines
	20 input files in total
	
1to1_19200/Florida_[id]-Florida_[id]-N19200-p050-simB.modified.sex.tab.gz
	input files, crossing scheme=1:1, N=19200 individuals
	four different mixtures of focal/non-focal lines 
	20 input files in total
	
1to1_300_30reps/Florida_111-Florida_[id]-N300-p050-simB-bigMix.modified.sex.tab.tar.gz
	infput files, crossing scheme=1:1, N=300 individuals, 30 different non-focal lines
	1 mixture of focal/non-focal lines
	30 input files in total

1tofew_300/Florida_[id]-5others-N300-p050-simC2.modified.sex.tab.tar.gz
	input files, crossing scheme=1:few, N=300 individuals
	four different mixtures of focal/non-focal lines
	4 input files in total 
	
1tomany_300/Florida_[id]-99others-N300-p050-simA.modified.sex.tab.tar.gz
	input files, crossing scheme=1:many, N=300 individuals
	four different focal lines
	4 input files in total 

dil_300/Base-100lines-N300-simE.modified.sex.tab.tar.gz
	input file, crossing scheme=dil:st & dil:mt, N=300 individuals
	100 different founder lines 
	1 input file in total
	serves as input file for the primary E&R
	secondary E&R are 50:50 mixtures of individuals from the input file, and evolved individuals
	in case the number of ancestral indiviuals for the secondary E&R is bigger than 300, each haplotype is added multiple times

Details regarding the different crossing schemes can be found in the main manuscript, Material & Methods & Figure 1

Details regarding the original haplotype sequences can be found in: https://doi.org/10.1093/gbe/evz082

20180816-createHaplos-simEandF.R
	Example code demonstrating how to generate haplotype files for Mimicree
	crossing scheme= dil:st, dil:mt, N=300 individuals
	uses: BaseFl-100Haplos.rds, BaseFl-names100Haplos.rds

BaseFl-100Haplos.rds
	haplotype sequences, chr 2L
BaseFl-names100Haplos.rds
	line identifiers