dist.dna: Calculate pairwise distances among DNA sequences
In lliu1871/phybase: Basic functions for phylogenetic analysis
dist.dna R Documentation
Calculate pairwise distances among DNA sequences
Description
Calculate pairwise distances among DNA sequences. The sites with missing characters are excluded.
Usage
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 with different nucleotides.
Value
The function returns a distance matrix.
Author(s)
Liang Liu lliu@uga.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
tree.upgma
Examples
data(dat.finch)
dist.dna(dat.finch$seq,nst=1)
lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.
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| dist.dna | R Documentation |
Calculate pairwise distances among DNA sequences
Description
Calculate pairwise distances among DNA sequences. The sites with missing characters are excluded.
Usage
dist.dna(sequences, nst = 0)
Arguments
sequences |
DNA sequences |
nst |
substitution model. 0:no model, 1:JC |
Details
If nst=0, the distance is equal to the proportion of sites with different nucleotides.
Value
The function returns a distance matrix.
Author(s)
Liang Liu lliu@uga.edu
References
Jukes, TH and Cantor, CR. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
See Also
tree.upgma
Examples
data(dat.finch)
dist.dna(dat.finch$seq,nst=1)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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