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. 

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 periods^{1} 
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 frequencies^{2} 
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 ratio^{3} 
1.8 
Codon models 
Rate variation among sites^{4} 
0.5 
Nuc/codon models 
Proportion of invariable sites 
0.2 
Nuc/codon models 


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

Arenas and Posada BMC Bioinformatics 2007 8:458 doi:10.1186/147121058458 