dist.hamming {phangorn} | R Documentation |
dist.hamming
and dist.logDet
compute pairwise distances
for an object of class phyDat
. dist.ml
fits distances
for amino acid models.
dist.hamming(x, ratio = TRUE) dist.logDet(x) dist.ml(x, model="JC69",...)
x |
an object of class dist.logDet |
ratio |
compute uncorrected ('p') distance or character difference. |
model |
One of "JC69", "WAG", "JTT", "LG" or "Dayhoff" |
... |
Further arguments passed to or from other methods. |
an object of class dist
Klaus Schliep K.P.Schliep@massey.ac.nz
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.
For more distance methods for nucleotide data see dist.dna
data(Laurasiatherian) dm1 <- dist.hamming(Laurasiatherian) tree1 <- NJ(dm1) dm2 <- dist.logDet(Laurasiatherian) tree2 <- NJ(dm2) treedist(tree1,tree2)