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

Open Data