7 Quick start guide

This section lists the main options of FREGENE. Although they are presented separately, they can be combined together. Running these lines in the Example directory, will only generate standard output but further outputs are available (see section 4.3).

• To run a single-subpopulation simulation without selection:
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml
• To run a selection model, use the -SELECT option, and define selection parameters in -p parameter file.
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml -SELECT
• To consider subpopulation structure in the population, use the -sub option, followed by the number of subpopulations and their size (here 2 subpopulations containing 1000, 4000 sequences, respectively):
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml -sub 2 1000 4000.
• To allow migration between subpopulations use the -tt option. Migration rates are specified in the -p parameter file:
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml -sub 2 1000 4000 -mg.
• To consider population growth use the -r option. The growth rate (here 1% per generation) is given as the argument of the option:
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml -r 0.01.
• To run a scaled simulation use the -scale option, this dramatically speeds the program up (here the scaling factor $\lambda$ is 10):
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml -scale 10.0
  This will leave the user with 10 times fewer sequences in the output file. To output the desired number of sequences , use the -scale_exp option, where the first argument is $\lambda$ (here = 10) and the second argument is the number of extra generations during which population expands to reach the desired size (here, 100 generations):
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml -scale_exp 10.0 100
• To enable self-reproduction, use the -SELFING option. The proportion of individuals coming from a single parent, the selfing fraction, (here 10%) is the argument of the option:
  ../Fregene_source/fregene -i data/in_example.xml -p data/par_example.xml -recomb data/recomb_example.xml -o data/rin_example.xml -SELFING 0.1

Below is an example of a more sophisticated simulation that implies the use of -sub, -subout and, -os options.

• Step 1: getting the initial panmictic population:
  The population size, specified in the input file, is 2,000 sequences. ../Fregene_source/fregene -i data/in_example.xml -p data/par_example1.xml -recomb data/recomb_example.xml -o data/rin_example.xml
  

• Step 2: Split in the population:
  2 subpopulations of 1,500 and 500 sequences are defined:
  ../Fregene_source/fregene -i data/rin_example.xml -p data/par_example_2.xml -recomb data/recomb_example.xml -o data/rin_2_example.xml -sub 2 1500 500
  Use -mg option if the population are not independent.
• Step 3: Extract the two subpopulations from the output:
  To achieve this, set the number of generations to 0 in par_example_3.xml.
  For the first subpopulation, run:
  ../Fregene_source/fregene -i data/rin_2_example.xml -p data/par_example_3.xml -recomb data/recomb_example.xml -o data/rin_Group1_example.xml -os 2 1500 0
  And for the second subpopulation:
  ../Fregene_source/fregene -i data/rin_2_example.xml -p data/par_example_3.xml -recomb data/recomb_example.xml -o data/rin_Group2_example.xml -os 2 0 500
  
• Step 4: Working on each subpopulation separately:
  To enable the allele counts, the swapping and the selected sites to be updated on each subpopulations, a final step is required. The number of generations for this step can be 0, if the user is interested by the subpopulation at the end of step 2. Extra generations are possible if the user wants each subpopulation to evolve independently:
  For the first subpopulation:
  ../Fregene_source/fregene -i data/rin_Group1_example.xml -p data/par_example_4.xml -recomb data/recomb_example.xml -o data/rin_final_Group1_example.xml -sub 1 1500
  And for the second subpopulation:
  ../Fregene_source/fregene -i data/rin_Group2_example.xml -p data/par_example_4.xml -recomb data/recomb_example.xml -o data/rin_final_Group2_example.xml -os 2 0 500