Usage Arguments Value Note Examples

1 |

`num.seqs` |
Number of simulated DNA sequences |

`num.haps` |
Number of simulated unique species' haplotypes |

`length.seqs` |
Basepair length of DNA sequences |

`nucl.freqs` |
Nucleotide frequency distribution vector of A, C, G, and T respectively |

`count.haps` |
Haplotype frequency distribution vector |

`subst.model` |
Model of DNA substitution |

`mu.rate` |
Overall nucleotide mutation rate/site/generation |

`transi.rate` |
Nucleotide transition rate/site/generation |

`transv.rate` |
Nucleotide transversion rate/site/generation |

A FASTA file of DNA sequences

`num.seqs`

must be greater than or equal to `num.haps`

.

Both `num.seqs`

and `num.haps`

must be greater than 1.

`nucl.freqs`

must have a length of four and its elements must sum to 1.

`count.haps`

must have a length of `num.haps`

and its elements must sum to `num.seqs`

.

`subst.model`

must be one of "JC69" (Jukes Cantor corrected p-distance), "K80" (Kimura-2-Parameter (K2P), "F81" (Felenstein) or "HKY85"(Hasegawa-Kishino-Yano)

`mu.rate`

must be specified for both "JC69" and "F81" models

`transi.rate`

and `transv.rate`

must be specified for both "K80" and "HKY85" models

All elements `nucl.freqs`

must be equal to 0.25 when `subst.model`

is either "JC69" or "K80"

All elements `nucl.freqs`

must differ from 0.25 when `subst.model`

is either "F81" or "HKY85"

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
# Simulate DNA sequences from the 5'-COI DNA barcode region under a Jukes Cantor nucleotide substitution model
num.seqs <- 100 # number of DNA sequences
num.haps <- 15 # number of haplotypes
length.seqs <- 658 # length of DNA sequences
count.haps <- c(60, rep(10, 2), rep(5, 2), rep(1, 5)) # haplotype frequency distribution
nucl.freqs <- rep(0.25, 4) # nucleotide frequency distribution
subst.model <- "JC69" # desired nucleotide substitution model
mu.rate <- 1e-3 # mutation rate
transi.rate <- NULL # transition rate
transv.rate <- NULL # transversion rate
sim.seqs(num.seqs = num.seqs, num.haps = num.haps, length.seqs = length.seqs, nucl.freqs = nucl.freqs, count.haps = count.haps, subst.model = subst.model, transi.rate = transi.rate, transv.rate = transv.rate)
``` |

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