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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
  1. 1from 1000 to 5000 effective size during 200 generations.
  2. 2can be specified for each codon position in codon models (3 × 4).
  3. 3dN/dS.
  4. 4shape of the gamma distribution.