TABLE 2.
Approximate run times for forward simulation programs and average value of summary statistics for forward and coalescent simulation programs
| Timee
|
||||||||
|---|---|---|---|---|---|---|---|---|
| 2Na | Generations | ub | rc | FORWSIMd | FREGENEf | FPGg | msh | Len (Mb) |
| a. Approximate run times for forward simulation programs | ||||||||
| 100 | 1,000 | 0.01 | 0.01 | 0.03 | 0.06 | 1.61 | 0.006 | 0.05 |
| 100 | 1,000 | 0.10 | 0.10 | 0.04 | 0.08 | 2.09 | 0.006 | 0.05 |
| 100 | 1,000 | 0.25 | 0.25 | 0.05 | 0.11 | 2.89 | 0.0075 | 0.05 |
| 1,000 | 10,000 | 0.01 | 0.01 | 1.74 | 4.71 | 265.06 | 0.006 | 0.05 |
| 1,000 | 10,000 | 0.10 | 0.10 | 2.85 | 18.50 | 450.90 | 0.035 | 1.00 |
| 1,000 | 10,000 | 0.25 | 0.25 | 6.51 | 43.79 | 1136.29 | 0.367 | 1.00 |
| 10,000 | 100,000 | 0.01 | 0.01 | 281.42 | 2241.59 | 45868.58 | 0.023 | 1.00 |
| 10,000 | 100,000 | 0.10 | 0.10 | 1153.41 | 13620.02 | — | 8.701 | 10.00 |
| 10,000 | 100,000 | 0.25 | 0.25 | 4470.48 | 34825.89 | — | 40.663 | 50.00 |
| FORWSIM
|
FREGENE
|
FPG
|
msh
|
||||||||
| 2N | Generations | u | r | E[S]i | E[H]j | E[S] | E[H] | E[S] | E[H] | E[S] | E[H] |
| b. Average value of summary statistics for forward and coalescent simulation programs | |||||||||||
| 1,000 | 10,000 | 0.01 | 0.01 | 71.250 | 16.066 | 69.637 | 16.242 | 71.551 | 16.078 | 71.016 | 15.916 |
| 1,000 | 10,000 | 0.10 | 0.10 | 708.614 | 19.612 | 704.071 | 19.635 | 708.089 | 19.656 | 706.603 | 19.538 |
Total number of chromosomes under the standard neutral Wright–Fisher model with constant population size and with uniform mutation and recombination rates.
Per-generation per-sequence mutation rate.
Per-generation per-sequence recombination rate.
FORWSIM is our C++ program freely available at http://people.cornell.edu/pages/bp85.
Time taken in seconds for a single run on a 2.2 Ghz 64-bit AMD processor machine with 8 GB of RAM.
FREGENE is a C++ program freely available at http://www.ebi.ac.uk/projects/BARGEN/download/FREGEN/fregeneweb.html.
FPG is a C program freely available at http://lifesci.rutgers.edu/∼heylab/ProgramsandData/Programs/FPG/FPG_Documentation.htm#FilesinthisPackage. For FPG, the number of chromosome segments was always fixed at 500.
ms is a C program that simulates data sets under the coalescent framework and is freely available at http://home.uchicago.edu/∼rhudson1/source.html. ms was run with population crossing-over rate ρ = 4Nr and population mutation rate θ = 4Nu and sample size of 20. (For details about ms, see Hudson 2002.)
Total number of SNPs for a sample size of 20 chromosomes. Average values are based on 1000 simulations.
Number of distinct haplotypes. Average values are based on a sample of 20 chromosomes and 1000 simulations.