GeneDrop v1.1.1
Author: James Elderfield (james_elderfield@hotmail.com)
Maintained by NIAB (ian.mackay@niab.com)

Description:
	- Runs gene dropping simulations for any supplied pedigree structure and genotype data.
	- Features/characteristics of simulation:
		- Can simulate multiple chromosomes
		- Cannot simulate loci with missing data, either put in dummy data or exclude from data-set
		- All loci are assumed to be biallelic, can use very tightly-linked markers to simulate polymorphic
		- Simulates only diploid organisms
		- Uses the Haldane Mapping Function to convert genetic distances into recombination fractions
		- Assumes uniform fitness landscape for simulated genotypes (i.e. only genetic drift, no selection)

Dependencies:
	- Windows OS
	- Dynamic Link Libraries included in the folder with the .exe
		- msvcp100.dll
		- msvcr100.dll
		- QtCore4.dll
		- QtGui4.dll
	- qjpeg4.dll needs to be within a folder called imageformats, imageformats should be in the same directory as the .exe
	
Maitenance:
	- The included source contains a project for use with QtCreator (http://qt.nokia.com/products/developer-tools/), the GeneDropWin.pro.user file should be deleted when moving between computers - else just open up the .pro file in QtCreator
	
Using GeneDrop:
	- Input genotypes should be denoted with a 0 representing one allele and a 1 the other
	- Formatting input data:
		- Example data files can be found in the ExampleInputFiles folder
		- For all input files the column titles do not matter, only their order
		- loci.csv (default name) should contain 3 columns: names of all the loci to be simulated, cumulative distance of the loci from the end of the chromosome, name of the chromosome the locus resides on
		- pedigree.csv (default name) should contain 4 columns: generation to which the invidual belongs (starting at 0, founder lines not entered here), name of individuals, name of first parent, name of second parent
		- founders.csv (default name) should contain 1 column giving the name of the founders and then a column for each locus with the corresponding genotype for that founder, a single digit is taken to be homozygous, heterozygotes should have their alleles separated by a '/' (i.e. 1/0)
	- The program is run just by double clicking GeneDrop.exe
	- Using the GUI
		- Type the number of wanted repetitions in the "Number of simulation runs" box
		- Check "Print results for every generation" if you are interested in the genotypes of individuals at every generation, leave unchecked if you only care about the final generation's genotypes
		- Click "Input Settings" to alter the files input into the program
		- "Go" starts the selected simulations, "Stop" will halt a currently running set of simulations
	- Getting the output data:
		- Output data is contained in Output files with timestamps
		- The first few lines give a quick summary of some of parameters for the dataset
		- The data is encoded in a trinary system for each locus in each individual (0- homozygous lack of marker, 1-heterozygous for marker, 2-homozygous presence of marker)