pair.dist.dna {phybase}R Documentation

Calculate pairwise distances among DNA sequences

Description

Calculate pairwise distances among DNA sequences. The DNA sequences are coded as 1:A, 2:G, 3:C, 4:T.

Usage

pair.dist.dna(sequences, nst = 0)

Arguments

sequences DNA sequences
nst substitution model. 0:no model, 1:JC

Details

If nst=0, the distance is equal to the proportion of sites having different nucleotides between two sequences.

Value

The function returns a distance matrix.

Author(s)

Liang Liu lliu@oeb.harvard.edu

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

upgma

Examples

tree<-"(((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01)#0.01;"
nodematrix<-read.tree.nodes(tree)$nodes
sequences<-sim.dna(nodematrix,10000,model=1)
pair.dist.dna(sequences,nst=1)

[Package phybase version 1.1 Index]