sim.dna: Simulate DNA sequences from substitution models
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Value Author(s) References See Also Examples

Simulate DNA sequences from a tree using substitution model

1 2	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))

`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

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

Liang Liu lliu@uga.edu

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.

sim.coaltree

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2
3

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)