Table 1 Key arguments for Recodon. The user can specify several parameters to implement different simulation scenarios. These arguments can be entered in the command line or read from a text file.
From: Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography
Parameter | Example value | Application |
|---|---|---|
Number of replicates | 1000 | All |
Sample size | 12 | All |
Number of sites (bp or codons) | 3000 | All |
Effective population size | 1000 | All |
Exponential growth rate | 2.1 × 10-5 | Demography |
Demographic periods1 | 1000 5000 200 | Demography |
Recombination rate | 5 × 10-6 | Recombination |
Migration rate | 1.2 × 10-4 | Migration |
Number of demes | 4 | Migration |
Mutation rate | 5.1 × 10-4 | All |
Nucleotide frequencies2 | 0.4 0.3 0.1 0.2 | Nuc/codon models |
Transition/transversion ratio | 2.1 | Nuc/codon models |
Relative substitution rates | 1.0 2.3 2.1 3.0 4.2 1.0 | Nuc/codon models |
Nonsynonymous/synonymous rate ratio3 | 1.8 | Codon models |
Rate variation among sites4 | 0.5 | Nuc/codon models |
Proportion of invariable sites | 0.2 | Nuc/codon models |