Description Usage Arguments Details Value Author(s) References See Also Examples
Calculate pairwise distances among DNA sequences. The DNA sequences are coded as 1:A, 2:G, 3:C, 4:T.
1 | pair.dist.dna(sequences, nst = 0)
|
sequences |
DNA sequences |
nst |
substitution model. 0:no model, 1:JC |
If nst=0, the distance is equal to the proportion of sites having different nucleotides between two sequences.
The function returns a distance matrix.
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.
1 2 3 4 5 | 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)
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