sim.dna: Simulate DNA sequences from substitution models

In lliu1871/phybase: Basic functions for phylogenetic analysis

Simulate DNA sequences from substitution models

Description

Simulate DNA sequences from a tree using substitution model

Usage

sim.dna(nodematrix,seqlength,model,kappa=2,rate=c(1,1,1,1,1,1),
frequency=c(1/4,1/4,1/4,1/4))

Arguments

nodematrix	the tree node matrix
seqlength	sequence length
model	1 JC, 2 H2P, 3 HKY, 4 GTR
kappa	the transition/transversion ratio
rate	the six rates used in GTR model
frequency	frequencies of four types of nucleotides

Value

The function returns DNA sequences simulated from the gene tree nodematrix. The sequences are coded as 1:A, 2:C, 3:G, 4:T.

Author(s)

Liang Liu [e-mail]

References

Jukes, TH and Cantor, CR. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.

See Also

sim.coaltree

Examples

tree<-"(((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635);"
nodematrix<-read.tree.nodes(tree)$nodes
sim.dna(nodematrix,100, model=2, kappa=4)

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.