dist.dna(x, model = "K80", variance = FALSE,
gamma = FALSE, pairwise.deletion = FALSE,
base.freq = NULL, as.matrix = FALSE)
as.matrix = TRUE
. If model = "BH87"
, a numeric
matrix is returned because the Barry--Hartigan distance is not
symmetric. If variance = TRUE
an attribute called "variance"
is
given to the returned object.
model
have been extensively described in the literature. A
brief description is given below; more details can be found in the
references.raw
,N
:variance
and
gamma
have no effect, but pairwise.deletion
can.} TS
, TV
:
JC69
:
K80
:
F81
:
K81
:
F84
:
BH87
:
T92
:
TN93
:
GG95
:
logdet
:dist.logdet
in
paralin
:
indel
:
indelblock
:-A-
and
A--
is 3 because there are three different blocks of gaps, whereas
the ``indel'' distance will be 2.}
Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368--376.
Felsenstein, J. and Churchill, G. A. (1996) A Hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution, 13, 93--104.
Galtier, N. and Gouy, M. (1995) Inferring phylogenies from DNA sequences of unequal base compositions. Proceedings of the National Academy of Sciences USA, 92, 11317--11321.
Gu, X. and Li, W.-H. (1996) Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies. Molecular Biology and Evolution, 13, 1375--1383.
Jukes, T. H. and Cantor, C. R. (1969) Evolution of protein molecules. in Mammalian Protein Metabolism, ed. Munro, H. N., pp. 21--132, New York: Academic Press.
Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111--120.
Kimura, M. (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proceedings of the National Academy of Sciences USA, 78, 454--458.
Jin, L. and Nei, M. (1990) Limitations of the evolutionary parsimony method of phylogenetic analysis. Molecular Biology and Evolution, 7, 82--102.
Lake, J. A. (1994) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proceedings of the National Academy of Sciences USA, 91, 1455--1459.
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.
McGuire, G., Prentice, M. J. and Wright, F. (1999). Improved error bounds for genetic distances from DNA sequences. Biometrics, 55, 1064--1070.
Tamura, K. (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution, 9, 678--687.
Tamura, K. and Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512--526.
read.GenBank
, read.dna
,
write.dna
, DNAbin
,
dist.gene
, cophenetic.phylo
,
dist