phangorn (version 0.0-2)

dist.hamming: Pairwise Distances from Sequences

Description

dist.hamming and dist.logDet compute pairwise distances for an object of class phyDat.

Usage

dist.hamming(x, ratio = TRUE)
dist.logDet(x)

Arguments

x

an object of class dist.logDet

ratio

compute uncorrected ('p') distance or character difference.

Value

• an object of class dist

References

Lockhart, P. J., Steel, M. A., Hendy, M. D. and Penny, D. (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution, 11, 605--602.

See Also

For more distance methods for nucleotide data see dist.dna

Examples

data(Laurasiatherian)
dm1 <- dist.hamming(Laurasiatherian)
tree1 <- NJ(dm1)
dm2 <- dist.logDet(Laurasiatherian)
tree2 <- NJ(dm2)
treedist(tree1,tree2)