TABLE C1

Approximate run-times for models with positive selection at multiple sites

Timef
2NaGenerationsu b r c h d s e NEWSELgFPGh
1,00010,0000.010.010.500.014.7882.06
1,00010,0000.100.100.500.015.70174.91
  • a Total number of chromosomes under the standard Wright–Fisher model with constant population size and uniform mutation and recombination rates.

  • b Per-generation per-sequence mutation rate.

  • c Per-generation per-sequence recombination rate.

  • d Dominance. A value of 0.5 denotes incomplete dominance in heterozygotes.

  • e Strength of selection per sequence.

  • f Approximate time taken for a single run on a machine with two 2.66 GHz dual-core Intel Xeon processors and 8 GB of RAM.

  • g NEWSEL is our C++ program freely available at http://people.cornell.edu/pages/bp85. We ran our simulation program under a simple model where 40 known sites are subject to positive selection and fitness effects are additive.

  • h FPG is a C program freely available at http://lifesci.rutgers.edu/∼heylab/ProgramsandData/Programs/FPG/FPG_Documentation.htm#FilesinthisPackage. FPG was run for roughly comparable parameters for the same model.