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 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 |
|
|
||
|
1from 1000 to 5000 effective size during 200 generations. 2can be specified for each codon position in codon models (3 × 4). 3dN/dS. 4shape of the gamma distribution. |
||
|
Arenas and Posada BMC Bioinformatics 2007 8:458 doi:10.1186/1471-2105-8-458 |
||
