sim.seqs: Simulate DNA sequences according to DNA substitution models

In HACSim: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment

Simulate DNA sequences according to DNA substitution models

Description

Simulates DNA sequences according to various DNA substitution models:

• Jukes-Cantor (1969)

• Kimura (1980)

• Felsenstein (1981)

• Hasegawa-Kishino-Yano (1985)

Output can then be passed to HACReal().

Usage

sim.seqs(num.seqs, num.haps, length.seqs, count.haps, nucl.freqs, 
codon.tbl = c("standard", "vertebrate mitochondrial", 
"invertebrate mitochondrial"), subst.model = c("JC69", "K80", "F81", "HKY85"), 
mu.rate, transi.rate, transv.rate)

Arguments

num.seqs	Number of simulated DNA sequences
num.haps	Number of simulated unique species' haplotypes
length.seqs	Basepair length of DNA sequences
count.haps	Haplotype frequency distribution vector
nucl.freqs	Nucleotide frequency distribution vector of A, C, G, and T respectively
codon.tbl	Codon table
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

Value

A FASTA file of DNA sequences

Note

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"

Examples

## Not run: 

# 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 <- 10 # number of haplotypes
length.seqs <- 658 # length of DNA sequences
count.haps <- c(65, 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
codon.tbl <- "vertebrate mitochondrial"
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, 
count.haps = count.haps, nucl.freqs = nucl.freqs, codon.tbl = codon.tbl, 
subst.model = subst.model, mu.rate = mu.rate, transi.rate = transi.rate, 
transv.rate = transv.rate)


## End(Not run)

HACSim documentation built on June 13, 2022, 9:05 a.m.