The program will print a table of the mean and standard deviation of fragment sizes and a table of the frequency distribution of each haplotype length from which a plot of the distribution can be created in Excel or similar

The following parameters can be set:

1) The numbers of crossovers per meiosis. 0, 1, 2 or 3 crossovers are permitted and the programme will randomly select one of these numbers at each meiosis.

2) The ratios of the different numbers of crossovers to each other. These can be entered in any format as decimal or whole numbers. The defaults are the mean ratios for mouse chromosomes from Broman et al Genetics 2002 160: 1123-1131.

3) An “interference interval” in which adjacent meioses may not occur in a double or triple crossover, eg no meioses within 10Mb of each other. Maximum 25

4) A mean interval between the markers used in the mapping panel. This will permit the program to predict the number of fragments that will be missed by those markers. The default is the mean distance between markers informative between A/J and C57BL/6 in the Illumina 1534 mapping set.

5) The number of founder haplotypes. This can be increased up to the population size to model multiway crosses or outbred populations

6) The population size. This population will be created at each meiosis at each generation and each replicate. A pair of chromosomes from within this population will be randomly selected for each meiosis. It may be more appropriate to vary this value and use a single replicate

7) Number retained at each generation. This can only be used when modelling a congenic line to specify the number of individuals that will be retained for generating the next generation

8) The length of the chromosome can be set, the default is 100Mb

9) The number of generations can be set up to an arbitrary maximum of 20.

Intercross or Backcross; In the backcross only chromosomes that are not under marker selection will be modelled; In the congenic the chromosome that is under selection will be modelled

Intercross ; Backcross ; Congenic ;

Ratios of crossovers per meiosis; Setting a ratio to 0 will mean that number of crossovers will not occur

No crossovers per meiosis One crossover per meiosis Two crossovers per meiosis Three crossovers per meiosis

Number of generations

Population size

Interference interval

Marker interval

Chromosome Size

Number of founder haplotypes

The following parameters are only used with a congenic model

Number of chromosomes retained at each generation;

Markers for negative selection upstream of congenic interval:

Markers for positive selection inside congenic interval

Markers for negative selection downstream of congenic interval

The program is written in Perl; a stand alone version is available for download here: Perl Script Download