MiscInput

• 1 Chromosome definition (--chromosome-definition)
• 2 Population size (--population-size)
• 3 Migration regime (--migration-regime)

1 Chromosome definition (--chromosome-definition)

For some species the reference sequences of chromosomes have been split into multiple parts. For example in D. melanogaster chromosome 2 has been split into 2L and 2R. Naive simulations would result in a random assortment between 2L and 2R. To avoid this potentially misleading behavior MimicrEE2 allows specifying the reference sequences that constitute a chromosome.

The chromosome definition must be provided as in the following example

--chromosome-definition "2=2L+2R,3=3L+3R"

or more generally it must be in the form

--chromosome-definition "new_chr=chr_part_1+chr_part_2,newchr=chr_part1+chr_part_2,..."

• new_chr: name of the full length chromosome
• chr_part_1: name of the first part
• chr_part_2: name of the second part
• chr_part_3: name of the third part and so on

Note: It is essential that you provide the chromosome parts in the correct order. For example 2=2R+2L would be wrong as this would concatenate the telomeric region of 2R with the centromeric region of 2L.
Note: It is possible to provide more than two parts of chromosomes e.g.: 3=3L+3M+3R
Note: If no chromosome definition is provided random assortment between reference sequences is assumed.

2 Population size (--population-size)

1   2000
20  1000
40  1500
60  2000

• col1: generation
• col2: population size (number of diploid individuals)

Note A population size must be provided for the first generation
Note For not provided generations the population size of the next closest previous generation is used
Note if no population size file is provided the population size of the base population will be used

3 Migration regime (--migration-regime)

MimicrEE2 allows simulating migration from a source population to the evolving populations. Per default the not-evolved base population acts as the source population, but different source populations may be provided. Source populations must be MimicrEE2 haplotype files (see above). The population size of the source population must be larger or equal to the number of migrants. If the number of migrants is smaller than the source population, migrants will be randomly picked from the source population.

10  100
30  200
40  400 /Users/robertkofler/dev/mimicree2/testdata/migrants.haplotypes.gz
600 200 /Users/robertkofler/dev/mimicree2/testdata/more-migrants.haplotypes.gz

• col1: generation
• col2: the number of migrants; i.e. the number of individuals of the evolved population that will be replaced by migrants. An error will be thrown if this number exceed the number of diploid individuals in the source population
• col3: source population of the migrants [optional]; A haplotype file (see above) needs to be provided. If no file is provided the base population is used as source population.

Note: Per default no migrants will be used, i.e. zero migrants will be used for any generations without entry in the migration regime file.
Note: MimicrEE2 validates the existence of any provided haplotype only directly before it is needed. This allows providing haplotype files that do not yet exist, which for example allows to use files that are generate during the simulations.