mimicree2 Files

[README]
Information regarding the input files used for simulations with the software:
1)MimicrEE1
2)MimicrEE2
3)forqs
4)quantiNemo
5)SLiM2
6)FFPopSim

All files can be found here:https://sourceforge.net/projects/mimicree2/files/publication_files/

1)MimicrEE1:
	a) dmel.rr.txt: recombination map of Drosophila melanogaster (RRC estimates)
	b) mimicree_format_dgrp_snps_X_chromosome: 205 DGRP haplotypes used as input
	c) runmim1_time.py: Python script used to estimate time estimates for MimicrEE1 (Table 1)

2)MimicrEE2:
	a) comeron_sex_specific: recombination map of Drosophila melanogaster (Comeron estimates).Different recombination rates for males females and hermaphrodites were used
	b) chosen_loci_1locus_X: loci that were assigned with an effect size. The targets of selection in our hypothetical example
	c) mimicree_format_dgrp_snps_X_chromosome: 205 DGRP haplotypes used as input
	d) runmim_time.py: Python script used to estimate time estimates for MimicrEE2 (Table 1)
	e) selection_regime_08: selection regime used for the simulation of truncation selection for starvation resistance.
	f) sex_info: information regarding sex (proportion of males and females in the population)

3)forqs:
	a) 2L_rr_forqs: recombination map for chromosome arm 2L (Comeron estimates)
	b) 2R_rr_forqs: recombination map for chromosome arm 2R (Comeron estimates)
	c) 3L_rr_forqs: recombination map for chromosome arm 3L (Comeron estimates)
	d) 3R_rr_forqs: recombination map for chromosome arm 3R (Comeron estimates)
	e) X_rr_forqs: recombination map for chromosome arm X (Comeron estimates)
	f) forqs_dgrp_haps_10pops.zip: ms file with the base population haplotypes

4)quantiNemo:
	a) genetic_map_for_dgrp: artificial recombination map used for the simulation with quantiNemo
	b) qnhaps_dgrp_all: haplotypes of the base population 

5)SLiM2
	a) 2L_rr_slim: recombination map for chromosome arm 2L (Comeron estimates)
	b) 2R_rr_slim: recombination map for chromosome arm 2R (Comeron estimates)
	c) 3L_rr_slim: recombination map for chromosome arm 3L (Comeron estimates)
	d) 3R_rr_slim: recombination map for chromosome arm 3R (Comeron estimates)
	e) X_rr_slim: recombination map for chromosome arm X (Comeron estimates)
	d) dgrp_slim_final_bin.zip: zipped format of the binary file with the input information supported 
	    by SLiM

6)FFPopSim
	a) run_FFPopSim.py: Python script that generates a user-specified number of haplotypes and SNPs and then performs truncation selection simulations (allowing mating between the best 80% of the population) for 40 generations using FFPopSim.
	    Four targets of selection are assumed. If you want to run the script make sure that you use >3000000 SNPs, as the script currently uses an index 3000000 to specify a target of selection.
	    Changes can be easily performed. The script prints the current state of the population.