TE Population Simulator_Written by Elie Dolgin, modified by Sam Groth and now forked by Kamil S. Jaron
There are two slightly different versions of this program.
Equilibrium allows you to drop a certain number of TE families into the genome and let the genome equilibrate.
Invasion problems will allow you to run many simulations, where a single TE family is introduce in one copy to the genome. The genome may or may not already have families in there.
To compile:
Place folders (Equilibrium or Invasion_Probs) in the appropriate location. Within the folders, type the command make.
To run:
Within the folder, provide a command file titled: input.txt.
type the command within the folder (if you don’t have your path variable pointing to the folder)
./TE_Sim_invasion
or
./TE_Sim_equil
Input.txt details
Input.txt
Line 1: N: placeholder, i.e No. MUST BE ‘N’. Line 2: N (actual population size, not read by genome, read by main) Line 3: ut ( transposition rate u, read by genome) Line 4: vt (excision rate v, read by genome) Line 5: sa (a, selection parameter, read by genome) Line 6: sb (b, synergism within family selection parameter, read by genome) Line 7: faf (frequency affecting fitness (1.0 is default, allowing for some to be neutral for values <1.0) ,read by genome) Line 8: initial family count (initialTE, read by genome) Line 9: (old run parameter, leave at 0) Line 10: (generations)
Not in input (hardwired) in genome.cpp Numberofchromosomes Ploidy Chromlength Rec Rate:
To change the number per previous family to equilibrium values (if different): Population.cpp: Poisson(29) value can be changed to Poisson(x)
Regarding equilibrium vs. invasion In population.cpp n = initialTE (from input.txt via Genome.cpp)
if n=0 a for loop is cutout if n=1 or more, within whichFamily for loop# of TEs initiated for each family within the genome is set at rand.Poisson(29) or rand.Poisson(x) where x is family initial abundance
In genome is: recombination rate, chromosome number, chromosome length, ploidy