recom-sim is a tool based on Nielsen et al.'s HYBRIDLAB for simulating hybrids from the genetic data of two reference populations using allele frequencies. recom-sim allows for faster simulations, the inclusion of significantly more markers, and the creation of common introgression classes (F2, B2, B3) in one step. While mainly geared towards SNP data, any biallelic data in GENEPOP format can be used.
python recom-sim.py input_file.txt 1 --num-offs 1000 --out output_file.txt
Similar to HYBRIDLAB, recom-sim uses the GENEPOP format as input. Any variation of comma or newline separated loci, two or three digit alleles, and tab or space separated data is accepted. Ensure that only two populations are present in the file.
Usage: recom-sim [OPTIONS]
Positional
input_file file path to GENEPOP reference
introgression choice of {1,2,3}
Optional
--num-offs INT number of offspring to simulate (def = 100)
--p1name TEXT name for pop1, used to differentiate backcrosses (def = 'POP1')
--p2name TEXT name for pop2, used to differentiate backcrosses (def = 'POP2')
--exclude excludes reference populations from output file
--out TEXT output file name (def = 'out')
The positional argument 'introgression' signifies the generational level to simulate.
- Only F1 hybrids
- F1, F2, B2POP1, B2POP2 (backcrosses to both reference populations: F1 x POP1, F1 x POP2)
- F1, F2, B2POP1, B2POP2, B3POP1, B3POP2 (B2POP1 x POP1, B2POP2 x POP2)
R E F P O P 1 R E F P O P 2
| | \ / | |
| | \ / | |
Gen1 | | F1HYB | |
| | / | | \ | |
| | / | | \ | |
Gen2 | B2POP1 F2HYB B2POP2 |
| / \ |
| / \ |
Gen3 B3POP1 B3POP2
Other introgression classes can be simulated by editing the output and feeding it back into the program (e.g. inputing two 'populations' of F2 with an introgression level of 1 to get F3)
Nielsen, E. E., L. A. Bach and P. Kotlicki (2006). "HYBRIDLAB (version 1.0): a program for generating simulated hybrids from population samples." Molecular Ecology Notes. 6(4): 971-973